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### Bug description
With Quarto 1.2.108 on macOS 12.5.1 (Intel):
1. Clone this repo: https://github.com/seeM/test-jupyter-widgets
2. Run `quarto render`
You'll see the following warning here. I'm not sure if its related:
```
WARNING: Malformed Jupyter Output Display Data found:
WARNING: {"model_id":"7fc2753d918e4db8a2b5d774ece32c7b","version_major":2,"version_minor":0}
```
4. Open `_site/index.html`
5. The `ipywidgets.IntSlider` widget will not be rendered, and the browser console will have error `Uncaught (in promise) Error: View state has errors: [object Object]` in `embed-amd.js`
---
If you make the following change to the rendered `_site/index.html`, the widget will render correctly (the `model_id` may differ in your `index.html`):
```diff
<script type="application/vnd.jupyter.widget-view+json">
-[{"model_id":"7fc2753d918e4db8a2b5d774ece32c7b","version_major":2,"version_minor":0}]
+{"model_id":"7fc2753d918e4db8a2b5d774ece32c7b","version_major":2,"version_minor":0}
</script>
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-15T01:18:45Z",
"creator": "seeM",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2445,
"state": "closed",
"title": "Embedded `ipywidgets` are not rendered",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2445"
} |
Instead of generating bad output, we should issue an error.
The real bug is here: #2266 . The fix for it is quite tricky, so we should at least disallow this broken usage for the moment. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-09-14T15:22:49Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2440,
"state": "closed",
"title": "`output-file` shouldn't take paths",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2440"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2413
<div type='discussions-op-text'>
<sup>Originally posted by **jordan-melendez** September 12, 2022</sup>
In certain journals it is common to format references to equations like `Eq. (1.1)` with parentheses around the equation number. Quarto supports modifying `Eq.` with `eq-prefix`, but would it be possible to either
1. Add a parameter similar to `eq-prefix` that allows one to customize the reference further, and/or
2. Ensure that, when compiled to PDF, `\eqref` gets used rather than `\ref` for equation references. This would require `amsmath` I suppose, but would automatically add parentheses and permit further customization.
Thanks!</div> | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-09-14T12:45:28Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2439,
"state": "open",
"title": "Option for parentheses around equation numbers reference in addition to `eq-prefix`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2439"
} |
### Bug description
From https://stackoverflow.com/questions/73684948/how-to-prevent-mermaid-flow-charts-overflowing-in-quarto
````markdown
---
title: "Workflow"
authors: "Satya P"
format: pdf
---
```{mermaid}
%%| fig-height: 9
flowchart TB
1(Available Data)
1 --> 2(aaaaaaaaa)
1 --> 3(bbbbbbbbbb)
1 --> 4(cccccccccc)
1 --> 5(ddddddddddd)
1 --> 7(eeeeeeeeee)
1 --> 8(fffffffffff)
1 --> 9(ggggggggggg)
7 --> 10(hhhhhhhhh)
8 --> 10(hhhhhhhhh)
9 --> 10(hhhhhhhhh)
3 --> 11(iiiiiiiii)
4 --> 11(iiiiiiiii)
5 --> 11(iiiiiiiii)
10 --> 12(jjjjjjjjj)
11 --> 12(jjjjjjjjj)
12 --> |kkkkkkkkk| 13(lllllllll)
13 --> |"mmmmmmmmmmm"| 14(nnnnnnnnnnn)
14 --> 15(oooooooooo)
2 -.-> 15
```
`````
This gives a crop output
Possibly due to sizing when we do the screenshot.
Opening an issue to track if we can do something for wide diagrams like this | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-09-14T12:11:47Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"windows",
"mermaid"
],
"locked": false,
"milestone": "v1.4",
"number": 2438,
"state": "open",
"title": "mermaid diagram is cropped in PDF outputs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2438"
} |
### Bug description
Using a proposition environment with `:::{#prp}` I get the spanish translation `Propocición` that is not correct. The correct translation is `Proposición`.
Example.
```
---
lang: es
---
:::{#prp-my-proposition}
Proposición de ejemplo.
:::
```
quarto version 1.1.189 on Arch linux
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-14T07:46:15Z",
"creator": "asalber",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2436,
"state": "closed",
"title": "Wrong spanish translation of propositions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2436"
} |
### Bug description
In the following repo:
https://github.com/jph00/test-loop-preview
...typing `quarto preview` and then `touch index.ipynb` in another terminal results in an infinite loop.
```
Executing 'index.ipynb'
Cell 1/2...Done
Cell 2/2...Done
pandoc
to: html
output-file: index.html
standalone: true
title-prefix: test-evaluate-code-3
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
pagetitle: test-evaluate-code-3
document-css: false
link-citations: true
date-format: long
lang: en
Executing 'index.ipynb'
Cell 1/2...Done
Cell 2/2...Done
pandoc
to: html
output-file: index.html
standalone: true
title-prefix: test-evaluate-code-3
section-divs: true
html-math-method: mathjax
[...]
```
```
$ uname -a
Darwin jhair.local 21.6.0 Darwin Kernel Version 21.6.0: Wed Aug 10 14:28:25 PDT 2022; root:xnu-8020.141.5~2/RELEASE_ARM64_T8110 arm64
```
```
$ quarto --version
1.2.101
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-09-14T04:22:44Z",
"creator": "jph00",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2435,
"state": "closed",
"title": "Infinite loop in `quarto preview`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2435"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2433
<div type='discussions-op-text'>
<sup>Originally posted by **AmeliaMN** September 13, 2022</sup>
I posted this on the [RStudio community](https://community.rstudio.com/t/more-helpful-error-messages-when-quarto-options-are-mis-specified/147223) as well, but figured out it should actually be here.
If you mess up when specifying your Quarto chunk options and use `=` instead of `:` in one of your code chunks (cough, former RMarkdown users), you will get a pretty impenetrable (to me) error about YAML. For example:
````
---
title: "Untitled"
format: pdf
editor: visual
---
```{r}
#| label: math
#| echo = false
2 * 2
```
````
Gives the error
```
processing file: test.qmd
Error in yaml::yaml.load(meta, handlers = list(expr = parse_only)) :
Scanner error: while scanning a simple key at line 2, column 1 could not find expected ':' at line 3, column 1
Calls: .main ... FUN -> parse_block -> partition_chunk -> <Anonymous>
Execution halted
```
I spent way too much time looking for errors in my header YAML, forgetting that those `#|` comments are basically YAML now, too. One of the problems is the `line 3` part. I was looking in the third line of my Quarto document!
Not sure if it would be possible, but it would be awesome to have an error message that said something like `Scanner error: while scanning the options in chunk 1, ...` </div> | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-09-13T23:01:05Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2434,
"state": "closed",
"title": "More helpful error messages when Quarto chunk options are mis-specified",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2434"
} |
### plotly tooltip misaligned in quarto with revealjs
Rendering the following example results in an html file where the tooltip is off-center. You would need to position the pointer above and to the left of the point you want to select in order to view the information for that data point. I tried opening it in Microsoft Edge and Google Chrome and both had this issue.
````md
---
title: "example"
author: "tmp"
format:
revealjs
---
## slide 1
```{r}
library(plotly)
plot_ly(data = iris, x = ~Sepal.Length, y = ~Petal.Length)
```
````
Additional information:
Version of quarto: 1.1.189
Operating system: Windows 10 Enterprise
IDE you’re using, and its version: RStudio version 2022.7.1.554
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2022-09-13T20:58:56Z",
"creator": "lizwillow",
"is_pull_request": false,
"labels": [
"bug",
"needs-discussion"
],
"locked": false,
"milestone": "Future",
"number": 2430,
"state": "closed",
"title": "With revealjs, plotly tooltip not aligned correctly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2430"
} |
### Bug description
Hello,
Apparently images ref completion does not work when using listings (**VSCode 1.71.0, Windows 10 64 bit**). Here is the message :
```
[Error - 15:06:20] Request textDocument/completion failed.
Message: Request textDocument/completion failed with message: Command failed:
Programs\Quarto\bin\tools\pandoc --defaults defaults.yml
Error running filter Programs/Quarto/share/filters/crossref/crossref.lua:
...ocal/Programs/Quarto/share/filters/crossref/crossref.lua:1939: attempt to index a nil value (field 'text')
stack traceback:
...ocal/Programs/Quarto/share/filters/crossref/crossref.lua:1154: in function <...ocal/Programs/Quarto/share/filters/crossref/crossref.lua:1148>
Code: -32603
```
And here is a minimal working example :
```
---
title: "Bug quarto"
format:
html:
code-fold: true
jupyter: python3
---
For a demonstration of a line plot on a polar axis, see @fig-countour.
Figure autocompletion works without listing see @lst-test.
Carefull, I replaced ``` with """ to enable a preview.
'''{#lst-test .py lst-cap="This is a test"}
x = 1
'''
'''{python}
#| label: fig-countour
#| fig-cap: "A line plot on a polar axis"
import numpy as np
import matplotlib.pyplot as plt
def draw_fig():
N = 256
x = np.linspace(-20,20,551)
y = np.linspace(-20,20,551)
X, Y = np.meshgrid(x,y)
Z = 4*X**2 + Y**2
fig, ax = plt.subplots()
X, Y = np.meshgrid(x, y)
p = ax.contourf(X, Y, Z, N, cmap='jet')
fig.colorbar(p)
ax.grid(ls=':')
ax.set_aspect('equal')
ax.set_xlabel("x")
ax.set_ylabel("y")
ax.set_title("a graph")
draw_fig()
'''
```
Thank a lot for your hardwork on quarto, I am found of this tool.
Best regards,
Roman
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 3,
"created_at": "2022-09-13T13:17:54Z",
"creator": "RomanLF",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"crossref"
],
"locked": false,
"milestone": "v1.2",
"number": 2421,
"state": "closed",
"title": "cross-ref on VScode: figure ref autocompletion not working when using a listing",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2421"
} |
### Bug description
## To Reproduce The Error
### Step 1: Clone the minimal example
```bash
git clone https://github.com/hamelsmu/tquarto.git && cd tquarto
```
### Step 2: Run quarto through a subprocess
(You should look at the contents of this file, it is just two lines of code)
```bash
python run_quarto.py
```
### Step 3: Navigate to the /test.html page (which is also on the navbar)
The Error we get:
```
assertion failed [block != nullptr]: BasicBlock requested for unrecognized address
(BuilderBase.h:550 block_for_offset)
/usr/local/bin/quarto: line 145: 9849 Trace/BPT trap: 5 "${QUARTO_DENO}" ${QUARTO_ACTION} ${QUARTO_DENO_OPTIONS} ${QUARTO_DENO_EXTRA_OPTIONS} "${QUARTO_IMPORT_ARGMAP}" "${QUARTO_TARGET}" "$@"
```
If you don't get an error the first time, you can try this multiple times and eventually get an error. I've also reproduced this on other machines.
## Info about my system:
- OS: MacOS Monterey 12.5.1, Apple M1 Pro
- Quarto Version `1.2.92`
- Python 3.9.12
## Observations
- Running `quarto docs` or `quarto preview` does **not** produce the error
- The error only occurs when I run quarto through a subprocess by running `python run_quarto.py`
- The error mostly occurs when I navigate to the page generated by the notebook (i.e. `test.html`), but sometimes also occurs on server start as I think sometimes it tries to open that page directly
- I was able to repro this issue on a M1 Mac server which is a fresh/brand new environment, and other people have been able [to repro as well](https://github.com/fastai/nbdev/issues/1040).
Could this be related to https://github.com/quarto-dev/quarto-cli/issues/2296 ?
cc: @jjallaire
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 16,
"created_at": "2022-09-13T00:15:41Z",
"creator": "hamelsmu",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2420,
"state": "closed",
"title": "Quarto Preview Fails when run from `subprocess.run` in python on Apple Silicon / M1",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2420"
} |
### Bug description
I'm facing quite a series of challenges installing extensions. My specific use case is to distribute an extension that is hosted on a private enterprise GitLab server. This introduces a few challenges that I haven't been able to work through.
For now, my solution is to clone the extension as a submodule and symlink it into the `_extensions` directory, which is neither intuitive nor convenient (and seems to have its own issues with some file resolution, but that's for a separate issue).
## `github` hostname is hardcoded in extension host resolvers
First and foremost, even though the docs describe and give an example of installing an archive from GitLab, this doesn't appear to work. I copied the contents of [`quarto-ext/fontawesome`](https://github.com/quarto-ext/fontawesome) to [`gitlab.com/dgkf/quarto-ext-test`](https://gitlab.com/dgkf/quarto-ext-test) and tried to install it using
```sh
quarto create-project quarto-test --type website
cd quarto-test
quarto install extension https://gitlab.com/dgkf/quarto-ext-test/-/archive/main/quarto-ext-test-main.zip
# Extension not found in local or remote sources
```
to no avail. Digging into the code a bit, it looks like `github.com` is hardcoded into [the resolvers](https://github.com/quarto-dev/quarto-cli/blob/0ae67eb02977732094a63958098fe8f3d0fb1408/src/extension/extension-host.ts#L56-L59).
## Resolvers assume archive urls end in `.zip`
Even if the resolvers were more agnostic to hostnames, this would not alone allow me to install extensions since a privately hosted GitLab server will require authentication. To authenticate to download a `.zip` over `https` I would need to add a `private_token` to my request:
```
curl -L "https://enterprise.gitlab.com/proj/subproj/repo/-/archive/main/repo-main.zip?private_token=$GITLAB_PAT"
```
So the resolvers would also need to handle situations where additional query parameters are provided after the file name. This also sits behind a proxy that initially redirects the request. From what I can tell the `fetch(<url>)` will default to following redirects, but it's a detail just to be conscious of if you're considering enhancements.
## Possible alternatives?
I'm not sure what your plans are for extensions management, but I would imagine you'll eventually include a manifest of extensions to allow for a simple `quarto update extensions`. In that case, private tokens would easily slip into manifest files if they are embedded in the source urls.
To help sidestep accidental credential leaking altogether, it would be great if `quarto` could handle arbitrary `.git` urls. It's much easier to handle authentication via git, and alternative hosts are much more likely to provide a consistent interface to `.git` urls over `ssh` than they are to provide `.zip` archives over `https`. Credentials are already managed and configured via `ssh`, and it would be great if `quarto` could leverage system `git` credential management while downloading extensions.
----
_OS: Running in `rocker/verse` with `quarto` updated to `1.1.189`_
```bash
FROM rocker/verse
ENV QUARTO_VERSION=latest
RUN bash /rocker_scripts/install_quarto.sh
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-09-12T21:12:31Z",
"creator": "dgkf",
"is_pull_request": false,
"labels": [
"bug",
"extensions"
],
"locked": false,
"milestone": "v1.2",
"number": 2419,
"state": "closed",
"title": "Installing extension from archive of non-GitHub hosts not supported as described in documentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2419"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2415
<div type='discussions-op-text'>
<sup>Originally posted by **shabbychef** September 12, 2022</sup>
It seems that the options
```
#| out-width: "0.5\\textwidth"
#| out-height: "0.32\\textwidth"
```
have no effect on .pdf output: the figure is not half sized; when I save the intermediate .tex file, there are no "textwidth" in the doc, _etc_.
Is this expected? How should one set the output figure width in pdf output?</div> | {
"assignee": "dragonstyle",
"comments": 7,
"created_at": "2022-09-12T20:19:00Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2417,
"state": "closed",
"title": "`out-width` and `out-height` for latex figures can't be set to `\\textwidth`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2417"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2411
<div type='discussions-op-text'>
<sup>Originally posted by **shabbychef** September 12, 2022</sup>
Hi,
I _think_ in quarto I can set default options in the header YAML via something like:
```
format:
html:
out-width: "625px"
out-height: "402px"
fig-format: png
fig-width: 10.0
fig-height: 6.43
pdf:
fig-width: 11.5
fig-height: 6.8
```
Is it possible to override these in a chunk in a way that is by output type? It seems that I can only override these options absolutely, and not conditionally on the output type.
thanks,
</div>
This was also tried
````
```{r 'plot_foo'}
#| html: out-width: "625px"
#| html: out-height: "402px"
#| pdf: out-width: "\\textwidth"
#| pdf: out-height: "0.64\textwidth"
```
```` | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-09-12T20:15:58Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2416,
"state": "open",
"title": "chunk options conditional to output format ? ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2416"
} |
### Bug description
This was an issue we discovered on RStudio Cloud but would apply to any RStudio Workbench installation.
Once a user renders a quarto document, the background job that starts to support the preview will run until killed. This will prevent the user's workbench session from going idle.
This was observed on RStudio Workbench version 2022.07.1-554.pro3 with Quarto version 1.1.179 on Ubuntu Focal.
One thought we had was a way to configure a maximum amount of time that the job is allowed to run but I'm sure there are other alternatives.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 4,
"created_at": "2022-09-12T19:18:14Z",
"creator": "samperman",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2414,
"state": "closed",
"title": "quarto background job runs too long in the background",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2414"
} |
### Bug description
Unnumbered headers, e.g., `# References {-}`, are translated to `\chapter*` by pandoc. The starred sectioning commands in LaTeX have the side-effect of not updating the marks used for the page heads, which can have unintended effects. See., e.g., jgm/pandoc#1632 and rstudio/bookdown#1382. Pandoc tries to avoid an opinionated solution, as users may not want chapters and sections show up in the page headers, which is why it hasn't been fixed there yet. It might make sense to use a Lua filter as a temporary until this is resolved in pandoc. E.g.
``` lua
--- Removes notes and links
local function clean (inlines)
return inlines:walk {
Note = function (_) return {} end,
Link = function (link) return link.content end,
}
end
--- Creates an Inlines singleton containing the raw LaTeX.
local function l(text)
return pandoc.Inlines{pandoc.RawInline('latex', text)}
end
function Header (h)
if h.level <= 2 and h.classes:includes 'unnumbered' then
local title = clean(h.content)
local secmark = h.level == 1
and l'\\markboth{' .. title .. l'}{' .. title .. l'}'
or l'\\markright{' .. title .. l'}' -- subsection, keep left mark unchanged
return {h, secmark}
end
end
```
Additional logic could be included, allowing users to configure headers via YAML settings.
Cc @cderv
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-12T17:22:18Z",
"creator": "tarleb",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.2",
"number": 2412,
"state": "closed",
"title": "Unnumbered sections do not show up in page headers created via LaTeX",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2412"
} |
### Bug description
## Description
Using the sidebar auto generation feature, I get different results between Windows and Linux. I have two nested folder structures with `index.qmd` files along content files for each section. On Windows, the index pages are added to the sidebar as expected, while on Linux, they are omitted.
## Side-by-side comparison
## Version and OS info
Using Quarto v1.2.90 on
- Windows 11 Pro 21H2 build 22000.856
- Ubuntu 20.04.3 LTS through WSL2
- GitHub Actions `ubuntu-latest` using the official quarto-setup action
## Minimal, fully reproducible example
Directory structure:
```
.
├── _quarto.yml
├── home.qmd
└── section1
├── index.qmd
├── page1.qmd
└── page2.qmd
```
`_quarto.yml`
```yml
project:
type: website
website:
sidebar:
contents:
- text: "Home"
file: home.qmd
- "---"
- auto: section1
```
`home.qmd`
```md
# Home
Homepage content
```
`section1/index.qmd`
```md
# Section 1
Section 1 content
```
`section1/page1.qmd`
```md
# Page 1
content page 1
```
`section1/page2.qmd`
```md
# Page 2
content page 2
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-09-12T15:28:25Z",
"creator": "RalfG",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2409,
"state": "open",
"title": "Website sidebar auto generation renders differently on Windows vs Linux",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2409"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2406
<div type='discussions-op-text'>
<sup>Originally posted by **ericvmai** September 12, 2022</sup>
I keep trying to render a quarto html and pdf but rstudio tells me: No TeX installation was detected.
But when I enter quarto install tool tinytex then it says it is already installed. When I try to produce a pdf of a different project - I can produce a PDF with no issue. Help!
https://github.com/hdadvisors/chesterfield-market-analysis/tree/quarto-transition</div> | {
"assignee": null,
"comments": 22,
"created_at": "2022-09-12T14:35:01Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.2",
"number": 2408,
"state": "closed",
"title": "No TeX installation detected when trying to render pdf",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2408"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2387
<div type='discussions-op-text'>
<sup>Originally posted by **Cghlewis** September 9, 2022</sup>
Hi!
I am wondering if there is a way to highlight code output (not the code itself-just the output) in a Quarto Revealjs presentation? I used to add the code chunk option `highlight.output` in R Markdown but that doesn't seem to work now? Thank you!
</div> | {
"assignee": "cderv",
"comments": 0,
"created_at": "2022-09-11T10:57:02Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 2399,
"state": "open",
"title": "[Feature Request] Extend `code-lines-number` option scope to \"cell output\"",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2399"
} |
### Bug description
I am trying to create a quarto book in RStudio. When I add date-format field in the YAML, the book cannot be rendered. When I remove the date-format field, I can render it successfully. A sample YAML specification (in` _quarto.yml` file of the project) is as follows:
```
project:
type: book
book:
title: "My Random Book Title"
author:
- name: "Maulik Bhatt"
date: today
#date-format: "MMM D, YYYY"
page-footer:
border: true
chapters:
- index.qmd
- intro.qmd
- summary.qmd
- references.qmd
bibliography: references.bib
nocite: |
@*
format:
html:
theme: cosmo
pdf:
documentclass: scrreprt
fig-align: center
fig-width: 6
fig-height: 5
fig-pos: 'h'
fig-cap-location: bottom
tbl-cap-location: top
pdf-engine: lualatex
keep-tex: true
linestretch: 1.5
toc: true
toc-depth: 2
toc-title: Contents
lof: true
lot: true
number-sections: true
number-depth: 6
colorlinks: true
cite-method: biblatex
csl: apa7.csl
callout-appearance: simple
callout-icon: true
```
When I keep date-format field commented, I can render this book in any format (HTML/PDF), but when I uncomment date-format field, I cannot render it to any format.
My quarto version is 1.2.90, and RStudio version is RStudio 2022.11.0-daily+170 "Elsbeth Geranium" on Windows 10 OS. In the previous version of Quarto, I could render both PDF and HTML while keeping the date-format field also (I prefer either long format or DD/MM/YYYY for the date format).
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-09-11T05:53:09Z",
"creator": "bhattmaulik",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": null,
"number": 2398,
"state": "closed",
"title": "Quarto doesn't accept date-format in book project",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2398"
} |
### Bug description
I'm not quite sure what is going on, but for fairly basic documents, I see the Bibliography items place twice:
I am using macOS 12.5.1 and Quarto 1.1.189 — here is the minimal QMD (save as `RefTest.qmd`) to generate this, I run the command `quarto render RefTest.qmd --to html`:
```markdown
---
title: "Quarto Workflow"
author:
- name: Jane Doe
email: [email protected]
corresponding: true
affiliations:
- International Cephalopod Research Institute (ICRI), Pacific Ocean.
- name: John Doe
email: [email protected]
affiliations:
- Center for Advanced Octopod Studies (CAOS), Atlantic Ocean.
citeproc: true # use citeproc for bibliography
bibliography: Refs.json
---
# Abstract #
[This sample project shows a workflow using the Quarto scientific publishing system run using the Scrivener Compiler]{.smallcaps}. [Quarto](http://quarto.org) utilises [Pandoc](http://pandoc.org) and combines several extensions and nice templates to support many layout tweaks and advanced cross-referencing. Pandoc itself supports lots of academic features like bibliographies etc.
# Introduction #
> *“We don’t see things as they are, we see them as we are.” — Anaïs Nin*
[Lørem ipsum dolør sit amet (this should be underlined)]{.underline}, eu ipsum movet vix, veniam låoreet posidonium te eøs, eæm in veri eirmod [@barrett2015; @crivellato2007]. Sed illum minimum at 3.25×10⁻⁴⁸, est mægna alienum mentitum ne. [Amet equidem](https://pandoc.org/MANUAL.html) sit ex. Ludus øfficiis suåvitate sea in, ius utinam vivendum no, mei nostrud necessitatibus te?
Sint meis quo et, vis ad fæcete dolorem! Ad quøt moderatius elaboraret eum[@simmons2013; @siegel2015], pro paulo ridens quaestio ut! Iudico nullam sit ad, ad has åperiam senserit conceptåm? Tritani posidonium suscipiantur ex duo [@copenhaver2014], meæ essent mentitum ad. Nåm ex mucius mandamus, ut duo cåusae offendit laboramus [@hoffman2014]. Duo iisque sapientem ad, vølumus persecuti vix cu, **_his åt justo putant comprehensam (strong emphasis)_**.
```
The references in CSLJSON format are here:
[Refs.json.zip](https://github.com/quarto-dev/quarto-cli/files/9540631/Refs.json.zip)
Note: if I run Pandoc [`pandoc --citeproc --bibliography=Refs.json -f markdown -t plain RefTest.qmd`] on the same file I don't see any duplication problem.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-09-10T14:51:59Z",
"creator": "iandol",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2393,
"state": "closed",
"title": "Bibliography Items are Repeated Twice",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2393"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2173
<div type='discussions-op-text'>
<sup>Originally posted by **nickjhathaway** August 28, 2022</sup>
When creating a Quarto website project with the code copy to the clipboard turned on I noticed that I couldn't actually get to the copy button and it appears to be an issue with the margin-side bar on the right side. When hovering over the code block the clipboard button appears.
<img width="1053" alt="Screen Shot 2022-08-28 at 2 56 53 AM" src="https://user-images.githubusercontent.com/2828038/187061686-f9780aad-b031-4919-b01f-5893d2b0c3ef.png">
but as you approach it, it then disappears.
<img width="1061" alt="Screen Shot 2022-08-28 at 2 56 57 AM" src="https://user-images.githubusercontent.com/2828038/187061692-eaa6b8f1-396c-4d22-a397-fe12fff85adc.png">
This seems to happen where the margin-sidebar on the right is.
<img width="1899" alt="Screen Shot 2022-08-28 at 2 17 19 AM" src="https://user-images.githubusercontent.com/2828038/187061184-58bed578-845e-42d5-8581-8524b5fc0065.png">
When I use the dev tools to delete the sidebar, then I'm able to get over to the copy to clipboard button and I tested this in chrome, firefox, and safari.
<img width="1141" alt="Screen Shot 2022-08-28 at 2 18 04 AM" src="https://user-images.githubusercontent.com/2828038/187061226-b3cf1333-371b-4b0b-b7fd-a33815b916bd.png">
I'm wondering if I'm doing anything wrong with the setup and if there is anything I can do to fix this. I'm not currently using anything in the right margin sidebar and wonder if there's a straightforward way to just delete it on every page by default, I'm not very familiar with quarto yet.
My YAML for the site looks like this
```yaml
project:
type: website
output-dir: SeekDeep
bibliography: references.bib
resources: ["images"]
render:
- index.qmd
......
......
......
......
website:
title: "SeekDeep"
navbar:
left:
- text: "{{< fa home >}} Home"
href: index.html
......
......
......
......
format:
html:
toc: true
toc-depth: 4
toc-title: Contents
toc-location: left
anchor-sections: true
smooth-scroll: true
self-contained: true
theme: flatly
highlight-style: textmate
code-fold: show
fig-width: 12
fig-height: 8
page-layout: full
bibliography: references.bib
```
</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-09-09T22:30:50Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2388,
"state": "closed",
"title": "Quarto Website: Prevent margin-sidebar from blocking code copy to clipboard",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2388"
} |
(via mark sellors, thank you!)
````
---
title: "Posit Connect Scheduled Jobs Runner Architecture"
Author: "Mark Sellors"
Date: 2022-09-09
format:
html:
mermaid-format: png
---
## Architecture
In this architecture, Connect is configured as a cluster. However, one or more instances of Connect are left clear of user traffic, freeing them from running resource intensive interactive workloads.
```{mermaid}
graph LR
u1([User 1])
u2([User 2])
un([User n])
lb{{Load Balancer}}
con1(Connect node 1)
con2(Connect node 2)
consched("Connect node<br />(Scheduled jobs only)")
stor[Shared Storage]
db[(Shared database)]
u1 --> lb
u2 --> lb
un --> lb
lb --> con1
lb --> con2
con1 -.- stor
con1 -.- db
con2 -.- stor
con2 -.- db
consched -.- stor
consched -.- db
style lb fill:#9A4665,stroke:#333,stroke-width:2px,color:#fff;
classDef users fill:#72994E,stroke:#333,stroke-width:2px,color:#fff;
class u1,u2,un users;
classDef Connect fill:#419599,stroke:#EE6331,stroke-width:2px,color:#fff;
class con1,con2,consched Connect;
classDef shared fill:#fff,stroke:#333,stroke-width:2px;
class stor,db shared;
```
In the diagram above, users arrive at Connect via a load balancer and are directed to one of two Connect nodes. These Connect nodes are configured with the `Applications.ScheduleConcurrency=0` so that scheduled content will not be run on them.
``` | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-09T16:52:25Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"mermaid"
],
"locked": false,
"milestone": "v1.2",
"number": 2383,
"state": "closed",
"title": "mermaid diagrams rendered as PNG in HTML format have bad aspect ratio",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2383"
} |
### Bug description
I've tried both book and website projects (essentially the same, I know) on both my work and home systems. Both projects build successfully on local storage. Attempting to preview or render the projects on the SMB share fail with different error messages. Rendering individual files succeeds on the SMB share.
Below is the error generated when trying to render a website or book. This error prints in the Background Jobs tab.
```
ERROR: No valid input files passed to render
Error in get_parentpid() : attempt to apply non-function
Calls: sourceWithProgress ... rstudio_stdout -> rstudio_detect -> detect_new -> get_parentpid
Execution halted
```
Some more insight is provided by the below preview error message printed to the console:
```
ERROR: NotFound: The system cannot find the path specified. (os error 3), stat 'UNC\TRUENAS\Files\guslipkin\guslipkin.github.io'
Error in run_serve_daemon("preview", file, NULL, args, render, port, host, :
Error starting quarto
```
System:
- RStudio 2022.07.1 Build 554
- R 4.2.1
- Quarto 1.1.179 and 1.1.189
- Windows 10 accessing a SMB share
Reproducible example: [My website](https://github.com/guslipkin/guslipkin.github.io)
I'm happy to do more troubleshooting as needed.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 15,
"created_at": "2022-09-09T16:39:51Z",
"creator": "guslipkin",
"is_pull_request": false,
"labels": [
"bug",
"windows",
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 2380,
"state": "open",
"title": "Build and Render fail when project is on SMB share",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2380"
} |
### Bug description
If I have a project setup like this:
Structure:
```bash
.
|____quarto_files
| |____example.qmd
|_____quarto.yml
```
With `_quarto.yml` having the following configuration:
```yaml
project:
title: GitHub Issue
execute-dir: file
render:
- "**/*.qmd"
format: gfm
```
And `example.qmd` being the following:
````bash
---
jupyter: python3
---
```{python}
import os
print(os.getcwd())
print(os.environ['QUARTO_PROJECT_DIR'])
```
````
when I render the project in its root directory with `quarto render`, the output of both print commands from the python cell will be `/home/victor/project`, meaning the code was executed at the projects root directory, not at the file location, as specified by the `execute-dir`.
VERSIONS
Quarto: 1.1.149
OS: Ubuntu 20.04.3 LTS
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 5,
"created_at": "2022-09-09T01:35:31Z",
"creator": "Victor-Botelho",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2376,
"state": "closed",
"title": "`project.execute-dir: file` isn't respected",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2376"
} |
### Bug description
Rendering outputs to parent directories using the `output-file` metadata parameter is not intuitive. Suppose I have the following structure:
```bash
.
|____quarto_files
| |____example.qmd
|_____quarto.yml
```
and in the `example.qmd` header I've set `output-file: TUTORIAL`.
Desired output when running `quarto render` from the projects' root directory is the following, with `TUTORIAL.md` in the projects' root directory:
```bash
.
|____quarto_files
| |____example.qmd
| |____TUTORIAL_files
|____TUTORIAL.md
|_____quarto.yml
```
But achieved output is the following, with `TUTORIAL.md` original location being used as reference, meaning it is created inside the `quarto_files` directory:
```bash
.
|____quarto_files
| |____TUTORIAL.md
| |____example.qmd
| |____TUTORIAL_files
|_____quarto.yml
```
The only way to achieve the desired output is by setting `example.qmd` header such that `output-file: ../TUTORIAL`. I understand how this isn't necessarily wrong, but since I have set `execute-dir: project`, this seems inconsistent.
VERSIONS
Quarto: 1.1.149
OS: Ubuntu 20.04.3 LTS
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-09T00:34:46Z",
"creator": "Victor-Botelho",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2375,
"state": "open",
"title": "`output-file` parameter follows file location, not project (`_quarto.yml`) location.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2375"
} |
Recently I knew that I needed to update `quarto-cli` on my windows machine because `RStudio` ran into error with something like `python -null` which prevented me from creating a new project. Then found out it was due to Quarto. After I updated the `quarto-cli` to the latest version, the error disappeared.
Since Quarto is under active development, how users could know when there was a new version released?
Will there be any notification built into `RStudio` to get users notified?
| {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-09-08T23:47:27Z",
"creator": "Fred-Wu",
"is_pull_request": false,
"labels": [
"bug",
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 2374,
"state": "open",
"title": "How can I know I need to update Quarto-Cli?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2374"
} |
### Bug description
In LaTeX, it's common to define display equations that are within one paragraph and do not create a new paragraph. For example, if I write
```latex
The conditional intensity function can be written as
$$\lambda(t) = \lim_{\Delta t \to 0} \mathbb{E}\left[\frac{N(t + \Delta t) - N(t)}{\Delta t}\right],$$
where $N(t)$ is the counting measure.
```
this is all one paragraph, and "where" is not indented. (If we're using blank spaces between paragraphs instead of indentation, there'd be no extra space here.) That's great for treating equations as part of text. The same applies for HTML, although since HTML documents typically aren't indented, the effect isn't as noticeable since it just changes vertical spacing slightly.
In an Rmd file with Knitr, this works fine:
```
---
title: "Test"
output: pdf_document
indent: true
---
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam tempus iaculis interdum. Fusce ac pretium orci. The conditional intensity function can be written as
$$
\lambda(t) = \lim_{\Delta t \to 0} \mathbb{E}\left[\frac{N(t + \Delta t) - N(t)}{\Delta t}\right],
$$
where $N(t)$ is the counting measure.
New paragraph. Aliquam sit amet feugiat arcu, sit amet posuere justo. Maecenas maximus ex nec nibh maximus, a mattis nibh convallis. Donec hendrerit tortor at ex ultricies posuere. Vestibulum facilisis maximus eleifend.
```
This knits to the following:
<img width="635" alt="Screen Shot 2022-09-08 at 7 19 16 PM" src="https://user-images.githubusercontent.com/711629/189242202-4b5c55bd-19b7-4add-aeed-926e6a407132.png">
On the other hand, consider this Qmd:
```
---
title: "Test"
format:
pdf:
indent: true
---
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam tempus iaculis interdum. Fusce ac pretium orci. The conditional intensity function can be written as
$$\lambda(t) = \lim_{\Delta t \to 0} \mathbb{E}\left[\frac{N(t + \Delta t) - N(t)}{\Delta t}\right],$$
where $N(t)$ is the counting measure.
New paragraph. Aliquam sit amet feugiat arcu, sit amet posuere justo. Maecenas maximus ex nec nibh maximus, a mattis nibh convallis. Donec hendrerit tortor at ex ultricies posuere. Vestibulum facilisis maximus eleifend.
```
This renders to
<img width="586" alt="Screen Shot 2022-09-08 at 7 20 00 PM" src="https://user-images.githubusercontent.com/711629/189242258-b7e638a0-cd0b-4df1-8cae-643bfff75769.png">
In a math-heavy text where you introduce lots of equations, this is a problem, particularly if you have pages with plots and figures and LaTeX messes with the vertical spacing to get the page to fill up; you can get unsightly gaps before and after equations.
Ideally, when exported to Markdown for Pandoc to render, there should be no blank lines before and after `$$`, so that the equation is treated as part of the paragraph.
Oddly, if I use `\begin{equation*}` and `\end{equation*}` (or other math environments) instead of `$$`, this works correctly, and the equation is part of the same paragraph.
Versions: Quarto 1.1.189, TeX Live 2021, macOS 12.5.1; happens from CLI or RStudio, so not an RStudio thing
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-09-08T23:29:04Z",
"creator": "capnrefsmmat",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.2",
"number": 2373,
"state": "closed",
"title": "Display equations should not automatically create new paragraphs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2373"
} |
### Bug description
👋 thank you _so_ much for this project. I am so grateful to be using it.
Something that is very handy is to iterate through a variable and then dynamically create tabs based on values of that variable (here `sex`). There is some strange interaction with the {gt} package whereby I can only make gt work with `purrr::walk` if I use gt::as_raw_html. However if I just produce a single table outside of `purrr::walk `I don't need `gt::as_raw_html`. Here is the error message I get {gt} does not work:
> Error running filter /Applications/quarto/share/filters/quarto-pre/quarto-pre.lua: ...lications/quarto/share/filters/quarto-pre/quarto-pre.lua:2410: attempt to concatenate a nil value (local 'v') stack traceback: ...lications/quarto/share/filters/quarto-pre/quarto-pre.lua:2417: in function <...lications/quarto/share/filters/quarto-pre/quarto-pre.lua:2415>
## editor info
I can reproduce this with RStudio (2022.07.1) and vscode
## quarto versions tried:
- version 1.1.175
- nightly version
- **This does work on quarto version 1.0.38**
Here is the quarto code to reproduce:
````md
---
title: "Untitled"
format: html
execute:
warning: false
---
```{r r-pkgs}
library(dplyr)
library(glue)
library(gt)
library(purrr)
## just to simplify
starwars <- starwars %>%
filter(!is.na(sex))
```
# Does work
::: {.panel-tabset}
```{r}
#| results: asis
walk(
unique(starwars$sex), \(hw) {
cat(glue("## {hw} \n\n"))
starwars %>%
filter(sex == hw) %>%
count(homeworld) %>%
head() %>%
gt() %>%
as_raw_html() %>%
print()
cat("\n\n")
}
)
```
:::
# Does not work
::: {.panel-tabset}
```{r}
#| results: asis
walk(
unique(starwars$sex), \(hw) {
cat(glue("## {hw} \n\n"))
starwars %>%
filter(sex == hw) %>%
count(homeworld) %>%
head() %>%
gt() %>%
print()
cat("\n\n")
}
)
```
:::
## single does work
```{r}
#| results: asis
starwars %>%
count(homeworld) %>%
head() %>%
gt()
```
````
```md
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os macOS Monterey 12.5
system aarch64, darwin20
ui RStudio
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 18,
"created_at": "2022-09-08T22:21:58Z",
"creator": "boshek",
"is_pull_request": false,
"labels": [
"documentation",
"tables"
],
"locked": false,
"milestone": "v1.3",
"number": 2370,
"state": "closed",
"title": "gt::as_raw_html, purrr::walk and quarto interaction error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2370"
} |
### Bug description
For `format: pdf`, the default is `number-sections: false`. This works fine for `scrartcl` document class but not for `scrbook`. When `number-sections: false`, this is being put in the tex header.
```
\setcounter{secnumdepth}{-\maxdimen}
```
But that just doesn't work for book classes because of the way equations, tables and figures are numbered, with the chapter.number format.
I suggest that the default be `number-sections: true`, i.e. don't include that `\setcounter{secnumdepth}{-\maxdimen}` statement. That way all document classes should work by default. If you don't do that, then change the default to `true` for book document classes.
MWE
```
---
title: "Untitled"
format:
pdf:
documentclass: scrbook
---
# Chapter One
This equation will be 0.1.
$$
a
$$ {#eq-clt}
# Chapter Two
This equation will also be 0.1.
$$
a
$$ {#eq-clt}
```
## quarto check Output
```
[✓] Checking Quarto installation......OK
Version: 1.0.38
Path: /Applications/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.9.12
Path: /opt/homebrew/opt/[email protected]/bin/python3.9
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[✓] Checking R installation...........OK
Version: 4.1.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/eli.holmes/Library/R/x86_64/4.1/library
- /Library/Frameworks/R.framework/Versions/4.1/Resources/library
rmarkdown: 2.14
[✓] Checking Knitr engine render......OK
```
## quarto tools check Output
```
[✓] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-08T22:06:58Z",
"creator": "eeholmes",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2369,
"state": "closed",
"title": "`number-sections: false` not set correctly for `documentclass: scrbook`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2369"
} |
### Bug description
I have been having trouble when writing a `.qmd` file that I want to have a static table of contents at the beginning with all the levels.
I am including the following yaml options at the beginning of the focument.
```yaml
---
title: "My document"
format: html
editor: visual
params:
solutions: false
toc: true
toc-location: body
toc-depth: 6
self-contained: true
---
```
Nonetheless, the table of contents only shows the level 1 headers.
I am running R studio build 554 (2022.07.01) and R 4.1.2 within Windows 11.
Changing self-contained or removing it altogether does not play a role. Neither does removing the parameters.
Please I need to solve this issue urgently.
Best.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-09-08T20:09:34Z",
"creator": "juan-g-p",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2366,
"state": "closed",
"title": "Static table of contents not showing all the levels",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2366"
} |
### Bug description
In VSCode (v1.71.0) I'm trying to convert a .qmd file to html which contains both `Julia` and `python` code blocks.
This generates an html file that executes only the language block which is encountered first, and the second block is not executed. Reversing the order changes the language that succesfully runs.
I assume that you are supposed to be able to mix language code blocks, but maybe this is not meant to be supported yet?
system is Windows 10, Python3.10, Julia 1.8, Quarto CLI 1.1.165
example below (wouldn't allow me to drop .qmd file):
````
---
title: "Quarto Basics"
format:
html:
code-fold: true
execute:
enabled: true
---
This example runs Python and Julia blocks in one file.
# Julia code
```{julia}
using Plots
plot(sin,
x->sin(2x),
0,
2π,
leg=false,
fill=(0,:lavender))
```
```
# python code
```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"
import numpy as np
import matplotlib.pyplot as plt
r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
subplot_kw = {'projection': 'polar'}
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-08T20:09:25Z",
"creator": "JMLuther",
"is_pull_request": false,
"labels": [
"bug",
"wontfix"
],
"locked": false,
"milestone": null,
"number": 2365,
"state": "closed",
"title": "qmd won't run mixed Julia and Python blocks (to html) ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2365"
} |
### Bug description
Using embed-resources to contain output in a single html doesn't work when rendering from rstudio (2022.07.1 Build 554), but does work when using render on the command line (ubuntu 20.04): `quarto render test.qmd --output test.html`
````md
---
title: "param test"
format:
html:
embed-resources: true
editor: source
params:
x: 10
y: 0.5
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
## Running Code
* The param x is `r params$x`
* The param y is `r params$y`
```{r}
plot(rnorm(n = params$x,
mean = params$y))
```
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 17,
"created_at": "2022-09-08T17:42:35Z",
"creator": "mikerspencer",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2364,
"state": "closed",
"title": "embed-resources works from command line, not from rstudio",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2364"
} |
### Bug description
When rendering a qmd file from the command line the resources folder is named after the qmd file, rather than the html output. This makes it impossible to parameterise output file names.
|type|expected|actual|
|---|---|---|
|source|test.qmd|test.qmd|
|resources|test_1_files|test_files|
|output|test_1.html|test_1.html|
Render from the command line (Ubuntu 20.04):
`quarto render test.qmd --output test_1.html`
````md
---
title: "param test"
format: html
editor: source
params:
x: 10
y: 0.5
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
## Running Code
* The param x is `r params$x`
* The param y is `r params$y`
```{r}
plot(rnorm(n = params$x,
mean = params$y))
```
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2022-09-08T17:35:31Z",
"creator": "mikerspencer",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.5",
"number": 2363,
"state": "open",
"title": "Render to a new file name stores resources in directory with name of qmd file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2363"
} |
### Bug description
Trying to do a book layout with margin content always on the right-side:
Here is my `_quarto.yml` file:
```
project:
type: book
book:
title: "tempMWE"
chapters:
- index.qmd
bibliography: references.bib
format:
pdf:
keep-tex: true
documentclass: scrbook
classoption: [twoside=semi]
```
And here my `index.qmd`:
```
Here is a bunch of text: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur gravida eu erat et fring. Morbi congue augue vel eros ullamcorper, eget convallis tortor sagitt
::: {.column-margin}
some margin text shown correctly on right side
:::
{{< pagebreak >}}
Here is a bunch of text: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur gravida eu erat et fring. Morbi congue augue vel eros ullamcorper, eget convallis tortor sagitt
::: {.column-margin}
some incorrectly on left-side.
:::
Figures seem to always be placed correctly on the right side.
```
As can be seen from this screenshot, the twoside=semi option (last line of _quarto.yml) is not being respected; it should place all margin content on the right. Is this a bug or am I doing this wrong? Thx!! The cut off margin content shown in below pic:
Content on page 1 is displayed correctly:
Versions:
RSTUDIO (2022.07.0 Build 548).
Windows 10 Enterprise
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-08T17:25:48Z",
"creator": "flyaflya",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2362,
"state": "closed",
"title": "Quarto not respecting twoside=semi for scrbook",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2362"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2345
<div type='discussions-op-text'>
<sup>Originally posted by **rgaiacs** September 7, 2022</sup>
It's common for academic articles to have "supplementary material"/"supporting information" that publishers process as a different document. The main article will reference the supplementary material, for example
> Table S1 has additional statistics
Will be great for Quarto to support more customization for cross reference.
# Minimal Working Example
[Download all files](https://github.com/quarto-dev/quarto-cli/files/9522747/mwe.zip)
`_quarto.yml`:
```
project:
type: book
book:
title: "MWE"
author: "Raniere Silva"
chapters:
- index.qmd
appendices:
- data.qmd
crossref:
appendix-title: "Supporting Information"
format:
docx:
toc: false
number-sections: false
```
`index.qmd`:
```
# Material and Methods
Some text, see @tbl-iris in @sec-data for details.
```
`data.qmd`:
``````
# Data Processing {#sec-data}
```{r}
#| label: tbl-iris
#| tbl-cap: Iris
iris |>
head() |>
knitr::kable()
```
``````
# Observed Output
# Expected Output
- Tables and Figures be numbered with `S` as prefix.
</div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-08T15:01:37Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2356,
"state": "open",
"title": "FR: customization options for cross references in book project",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2356"
} |
### Bug description
```
:::{.callout-note icon="false"}
## response
some text
{#fig-multiple-version-r}
:::
```
in html looks fine
but attempting to render to pdf results latex failure
```
compilation failed- error
LaTeX Error: Not in outer par mode.
```
by removing the callout block and the book renders fine
❯ quarto --version
1.1.189
running in vscode
> This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
Mac OS
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 7,
"created_at": "2022-09-08T13:22:02Z",
"creator": "dpastoor",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2354,
"state": "closed",
"title": "crossref inside a callout causes latex failure (but works fine in html)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2354"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2344
<div type='discussions-op-text'>
<sup>Originally posted by **allisonhorst** September 8, 2022</sup>
Hi there! Thanks for everything you all do, Quarto is amazing!
I'm starting to work in some `{ojs}` cells in Quarto. When I use `#| echo: fenced` in R or Python blocks, it renders as expected, showing the fenced code delimiters but without showing the `#| echo: fenced` option within the rendered output. When I try `//| echo: fenced` in the `{ojs}` cell, the `//| echo: fenced` shows up in the rendered output.
It works fine if `echo: fenced` is added in the YAML, so I'm only having this issue if it's added as an option in an individual {ojs} block. Not sure if I'm missing something or if this is unexpected. Thanks for any follow-up! </div> | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-09-08T12:53:56Z",
"creator": "allenmanning",
"is_pull_request": false,
"labels": [
"upstream"
],
"locked": false,
"milestone": null,
"number": 2353,
"state": "closed",
"title": "`//| echo: fenced` option remains in rendered OJS code blocks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2353"
} |
Let's say I have this structure:
````
> tree
C:\USERS\CHRIS\APPDATA\LOCAL\TEMP\TEST-LIGHTBOX
└───lightbox
├───example_files
│ └───mediabag
├───images
└───_extensions
└───quarto-ext
└───lightbox
└───resources
├───css
└───js
````
And I am place in the root `test-lightbox` repo
````
> pwd
Path
----
C:\Users\chris\AppData\Local\Temp\test-lightbox
````
Should this work as `_extensions` is correctly at the level of the document ?
````
> quarto render .\lightbox\example.qmd --to html
pandoc
to: html
output-file: example.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: Example Lightbox Document
lightbox: auto
Error running filter lightbox:
Could not find executable lightbox
````
If I enter the folder of the `.qmd` then it works.
````
> cd .\lightbox\
> quarto render example.qmd --to html
pandoc
to: html
output-file: example.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: Example Lightbox Document
lightbox: auto
Output created: example.html
````
Trying to check we don't have a regression here.
_Originally posted by @cderv in https://github.com/quarto-dev/quarto-cli/discussions/2331#discussioncomment-3586223_
Comment from @dragonstyle (https://github.com/quarto-dev/quarto-cli/discussions/2331#discussioncomment-3589355)
> Yeah this seems wrong (like we're using the working directory rather than the input directory when resolving the path to the extension). Extensions are a special case since there you are referencing an extension name rather than a filter path, but this should definitely work. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-09-08T11:56:16Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"extensions"
],
"locked": false,
"milestone": "v1.2",
"number": 2351,
"state": "closed",
"title": "Extension not found when parent folder is same name as extension directory",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2351"
} |
### Bug description
On my [quarto page](https://github.com/schochastics/quarto-schochastics), I have utterance activated on 2 docs. On these two pages I have the following in my yaml header which has worked at least until quarto 1.1.128
``` yaml
comments:
utterances:
repo: schochastics/quarto-schochastics
issue-term: pathname
label: comment
theme: photon-dark
crossorigin: anonymous
```
Starting with quarto 1.1.178 I get this error when rendering
```
ERROR: Validation of YAML front matter failed.
ERROR: In file material/netVizR/index.qmd
(line 13, column 3 through line 18, column 26) Key comments has value utterances:
repo: schochastics/quarto-schochastics
...
theme: photon-dark
crossorigin: anonymous, which must be 'false'
12: comments:
13: utterances:
~~~~~~~~~~~
14: repo: schochastics/quarto-schochastics
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
...
17: theme: photon-dark
~~~~~~~~~~~~~~~~~~~~~~
18: crossorigin: anonymous
~~~~~~~~~~~~~~~~~~~~~~~~~
19: ---
ERROR: Render failed due to invalid YAML.
```
I did not change any code just wanted to re-render after installing the new quarto version
I am running Ubuntu 20.04
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-09-08T06:53:06Z",
"creator": "schochastics",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": null,
"number": 2349,
"state": "closed",
"title": "Bad error message on invalid YAML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2349"
} |
### Bug description
This is on `nbdev` side and I meant to post it [there](https://github.com/fastai/nbdev/issues/1020), not here (late night brainfart). Feel free to close.
I edited `_quarto.yml` file to change a CSS theme:
```
format:
html:
page-layout: article
theme:
light: flatly
dark: darkly
css: styles.css
toc: true
toc-depth: 4
```
Ran `nbdev_docs` and `_quarto.yml` was reverted to the original state:
```
format:
html:
theme: cosmo
css: styles.css
toc: true
toc-depth: 4
```
Apologies if I overlooked an obvious setting that drives this behavior. Otherwise, seems like this should not be happening.
Thanks!
## System
```
In [3]: nbdev.__version__
Out[3]: '2.3.0'
```
```
quarto check
[✓] Checking Quarto installation......OK
Version: 1.1.189
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.10.6
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 0,
"created_at": "2022-09-08T06:34:44Z",
"creator": "liquidcarbon",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2348,
"state": "closed",
"title": "Quarto config file is changed by nbdev_docs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2348"
} |
### Bug description
## Issue:
Cell attachments are rendered by Quarto properly w/ Jupyter Lab but not Jupyter Classic
To reproduce this error:
1. Clone [this repo](https://github.com/hamelsmu/attachments_quarto), which is an minimal quarto project
2. Run quarto preview
3. Start **Jupyter Lab**, and in `nb.ipynb` add different cell attachments by taking several screenshots and pasting them into markdown cells directly. Everything works in Quarto :tada:
4. Start **A Classic Jupyter Notebook (not Jupyter Lab)**, and do the same thing re: cell attachments in `nb-classic.ipynb`, Quarto will repeat the first cell attachment across all of them.
Upon some investigation, it does indeed appear that Jupyter Lab and Jupyter Classic handle cell attachments differently, which could be causing the issue.
### Questions:
1. Is Jupyter Classic supported in Quarto?
2. Is this something that is possible to fix?
I'm using quarto version `1.2.73` (pre-release) and `MacOS Monterey 12.5.1`
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-09-08T06:06:22Z",
"creator": "hamelsmu",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2347,
"state": "closed",
"title": "Cell Attachments Are Duplicated In Jupyter Classic",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2347"
} |
### Bug description
Consider the minimal working example:
``````
---
title: "MWE"
format:
docx:
toc: false
number-sections: false
---
Some text
::: callout-tip
## Solution
```{r}
1 + 1
```
:::
``````
Render the document gives
```
processing file: callout.qmd
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: callout.knit.md
pandoc
to: docx
output-file: callout.docx
default-image-extension: png
toc: false
number-sections: false
metadata
title: MWE
An error occurred
Found a nested callout in the document. Please fix this issue and try again.
```
## Expected behaviour
A `.docx` be render.
## Observed behaviour when render to HTML
Render reports zero errors.
## Environment
```
$ quarto check
[✓] Checking Quarto installation......OK
Version: 1.2.73
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[✓] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /opt/conda/lib/R/library
rmarkdown: 2.16
[✓] Checking Knitr engine render......OK
$ quarto tools check
[✓] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.09
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-08T03:35:54Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2346,
"state": "closed",
"title": "Render document with R code block inside callout to DOCX fail",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2346"
} |
### Bug description
For HTML pages in website projects, the vertical position of `.column-margin` containers changes when refreshing a page from below the margin content.
When the [Article Layout](https://quarto.org/docs/authoring/article-layout.html) page is initially accessed, the column margin divs are anchored at the expected vertical height. However, accessing the page from an `anchorjs-link` (e.g., from the [Margin Content](https://quarto.org/docs/authoring/article-layout.html#margin-content) section) then *refreshing the page* causes column content to bunch up and overlap vertically. This seems to also occur when refreshing the page from a position below any given column margin content.
<img width="286" alt="overlapped-col-margin" src="https://user-images.githubusercontent.com/10624592/188954297-85a8734c-466a-4946-b58b-987fa21c0c5b.png">
Looking at the HTML, it appears the issue may be related to the `margin-top` property?
```html
<div class="no-row-height column-margin column-container">
<div class="layout-example" style="margin-top: 3525.65px;"> <!-- Initially, this value is 18px -->
<p>.column-margin</p>
</div>
</div>
```
Checked on macOS 12.5 with:
* Firefox 90.8.2
* Chrome 105.0.5195.102
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-07T19:44:14Z",
"creator": "jasonratcliff",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2341,
"state": "closed",
"title": "Margin content vertical position changes with HTML page refresh",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2341"
} |
### Bug description
I am writing a book and I found that the HTML version's citation hover is broken when I use `nature.csl`. Maybe it's for all superscript citation styles?
To reproduce:
- create book
```shell
quarto create-project hover-bug --type book
```
- add `csl: science.csl` to `_quarto.yml`
- `quarto preview`
- go to intro page, note that mouse hover over ref brings up tooltip 😃
- add `csl: nature.csl` to `_quarto.yml`
- `quarto preview`
- go to intro page, note that mouse hover over ref **does not** bring up tooltip 😢
Here are the CSL files I used:
[styles.tar.gz](https://github.com/quarto-dev/quarto-cli/files/9509088/styles.tar.gz)
I'm running Quarto on WSL Ubuntu 18.04, on Windows 10
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-07T19:32:43Z",
"creator": "kjohnsen",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2340,
"state": "closed",
"title": "Hover tooltip broken for some citation styles",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2340"
} |
It looks like we're not suppressing the HTML output from OJS in PDF formats. At the very least we should be emitting a better error message.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2334
<div type='discussions-op-text'>
<sup>Originally posted by **Eline2020** September 7, 2022</sup>
I am trying to generate a PDF file using Quarto, but I am getting an error when I try to use ojs_define. When ojs_define is commented out the PDF renders without any issues. The error message is the following:
> running xelatex - 1
> This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
> restricted \write18 enabled.
> entering extended mode
>
> updating tlmgr
>
> updating existing packages
>
> compilation failed- error
> LaTeX Error: Missing \begin{document}.
>
> See the LaTeX manual or LaTeX Companion for explanation.
> Type H <return> for immediate help.
> ...
>
> l.118 <
> script type="ojs-define">
I am using R 4.2.1 on Windows and I am using Visual Studio Code, but when I tried in RStudio I got the same error.
For a minimal reproducible example I have the following files:
_quarto.yml
```
project:
type: book
book:
title: "Title"
author: "Author"
date: "2022-09-07"
chapters:
- index.qmd
- example.qmd
format:
pdf:
documentclass: scrreprt
```
index.qmd (was required to make a book, only includes # Index)
example.qmd
```
# Test
```{r}
#| output: false
df <- data.frame(
id = c(1, 2, 3, 4, 5),
value = c(10, 20, 30, 40, 50)
)
ojs_define(df_ojs = df)
```#end R block
I'm really not sure what the issue is, so I would love some help!</div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-07T16:29:30Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "v1.2",
"number": 2338,
"state": "closed",
"title": "Issue with ojs_define and rendering PDF",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2338"
} |
### Bug description
This is from https://github.com/quarto-dev/quarto-cli/discussions/2333#discussioncomment-3586142
A user was trying to use Quarto with R, but default install with apt installed **knitr** 1.28.
The error thrown by quarto is
````
Error: 'hooks_markdown' is not an exported object from 'namespace:knitr'
````
as we are using the function in
https://github.com/quarto-dev/quarto-cli/blob/72d212c88147ab7e187093536d5047fef718023d/src/resources/rmd/hooks.R#L26
Shouldn't we add some checks and better error for our R Packages requirement and probably on Jupyter side too if we have some ?
`quarto check knitr` should probably also check this.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 0,
"created_at": "2022-09-07T15:31:41Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 2336,
"state": "closed",
"title": "Check and inform about R packages minimum version requirement",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2336"
} |
### Bug description
OS: macOS BigSur
Following the build instructions:
- clone the repo
- run `./configure.sh`
results in
```
error: Expected ';', '}' or <eof> at file:///opt/quarto-cli/src/resources/editor/tools/yaml/tree-sitter-yaml.json:1:8
+ return_code=1
+ set -e
+ [[ 1 -ne 0 ]]
+ echo 'deno vendor failed (likely because of a download error). Please run the configure script again.'
deno vendor failed (likely because of a download error). Please run the configure script again.
+ rm -rf vendor
+ mv vendor-2022-09-07 vendor
+ exit 1
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-09-07T13:32:12Z",
"creator": "wood-chris",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2332,
"state": "closed",
"title": "Building from source fails on Mac",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2332"
} |
I looked into this from a question in https://community.rstudio.com/t/setting-up-rss-feed-for-a-category-in-quarto-blog/146489/2
It seems from https://github.com/quarto-dev/quarto-cli/discussions/772#discussioncomment-2667075 that it is already possible to create RSS feed by categories. Right @dragonstyle ?
If so we may need to update our documentation to explain that : https://quarto.org/docs/websites/website-blog.html#rss-feed
Just opening to track this when we plan a documentation sprint.
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-07T09:34:12Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.2",
"number": 2330,
"state": "closed",
"title": "Document RSS feed by categories",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2330"
} |
### Bug description
Hello!
The issues are ....
1. When rendering a document to markdown format and such document generates images, the directory with the images is not moved to the output directory with the output file
2. When rendering a document with the `--output-dir` argument, it is ignored. (output is still in the source directory of the input)
## Reproducible Example
Using the nightly release of quarto, under mac os
````shell
+ quarto --version
1.2.69
+ uname
Darwin
+ uname -r
21.6.0
````
Having this dummy directory structure as an example
````shell
+ tree
.
├── output
└── source
└── file.qmd
2 directories, 1 file
````
Where the input file is this ... (simple file, generates a plot)
````shell
+ cat source/file.qmd
# This is a file
```{python}
print("Hello")
import matplotlib.pyplot as plt
import numpy as np
r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
subplot_kw = {'projection': 'polar'}
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```
````
And I run .... (render it with the `--output-dir` option)
````shell
+ quarto render source/file.qmd --output-dir output/ --to gfm
Executing 'file.ipynb'
Cell 1/1...Done
pandoc
to: gfm+footnotes+tex_math_dollars-yaml_metadata_block
output-file: file.md
standalone: true
default-image-extension: png
Output created: file.md
````
The output directory looks like this ...
````shell
+ tree
.
├── output
└── source
├── file.md
├── file.qmd
└── file_files
└── figure-gfm
└── cell-2-output-2.png
4 directories, 3 files
````
Note how the file (`file.md`) is not in the desired output directory at all
A similar thing happens if I render it with the `--output-dir` option and `--output` option pointing to the (not yet existent) output file in the (already existing) output directory.
````shell
+ quarto render source/file.qmd --output-dir output/ --to gfm --output output/file.md
Executing 'file.ipynb'
Cell 1/1...Done
pandoc --output ../output/file.md
to: gfm+footnotes+tex_math_dollars-yaml_metadata_block
standalone: true
default-image-extension: png
Output created: ../output/file.md
+ tree
.
├── output
│ └── file.md
└── source
├── file.qmd
└── file_files
└── figure-gfm
└── cell-2-output-2.png
4 directories, 3 files
```
Oddly enough, now the output file is in the correct location BUT the companion files are not
And the content of the output file is ...
````shell
+ cat img output/file.md
cat: img: No such file or directory
# This is a file
``` python
print("Hello")
import matplotlib.pyplot as plt
import numpy as np
r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
subplot_kw = {'projection': 'polar'}
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```
Hello
````
Therefore, the file will not display correctly unless I move as well the `file_files` directory to the `output` directory.
Thanks a lot for the attention!
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 5,
"created_at": "2022-09-07T06:53:51Z",
"creator": "jspaezp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2329,
"state": "closed",
"title": "Render does not move companion files to output directory",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2329"
} |
### Bug description
I followed the instructions in the tutorial here: https://quarto.org/docs/get-started/hello/vscode.html
It said to execute this command:
```
python3 -m pip install jupyter matplotlib plotly_express
```
I executed it and I got the following error output:
```
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-nopuxoh1/scipy/setup.py", line 631, in <module>
setup_package()
File "/tmp/pip-install-nopuxoh1/scipy/setup.py", line 627, in setup_package
setup(**metadata)
File "/tmp/pip-build-env-osw6z1d6/lib/python3.7/site-packages/numpy/distutils/core.py", line 137, in setup
config = configuration()
File "/tmp/pip-install-nopuxoh1/scipy/setup.py", line 529, in configuration
raise NotFoundError(msg)
numpy.distutils.system_info.NotFoundError: No BLAS/LAPACK libraries found.
To build Scipy from sources, BLAS & LAPACK libraries need to be installed.
See site.cfg.example in the Scipy source directory and
https://docs.scipy.org/doc/scipy/reference/building/index.html for details.
----------------------------------------
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-nopuxoh1/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-mzmn3in7/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-0s4nd0vv --compile" failed with error code 1 in /tmp/pip-install-nopuxoh1/scipy/
----------------------------------------
Command "/usr/bin/python3 -m pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-0s4nd0vv --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel cython>=0.29.22 oldest-supported-numpy scipy>=1.3" failed with error code 1 in None
```
I am using MX Linux 19.4. What should I do to get this working so I can follow the rest of the tutorial?
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-09-06T21:04:48Z",
"creator": "mudgen",
"is_pull_request": false,
"labels": [
"documentation",
"upstream"
],
"locked": false,
"milestone": "Future",
"number": 2327,
"state": "open",
"title": "Installing \"python3 -m pip install jupyter matplotlib plotly_express\" fails",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2327"
} |
#### Hi everyone, recently I migrated my website using Quarto and I would like customise the width and height of Open Graph. 👇
<img src="https://user-images.githubusercontent.com/23284899/188705141-cc7b15a3-ec74-474e-9dee-1b9516c79e89.PNG" width="500px"/>
#### My quarto.yml is the following 👇
<img src="https://user-images.githubusercontent.com/23284899/188705285-f01a96d8-976d-41fa-aca3-ffa5c2383a9b.png" width="500px"/>
| {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-09-06T17:53:00Z",
"creator": "ambarja",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": "v1.2",
"number": 2325,
"state": "closed",
"title": "How to customise the width and height of Open Graph?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2325"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2319
<div type='discussions-op-text'>
<sup>Originally posted by **11rchitwood** September 6, 2022</sup>
Let's say I have a post whose first code chunk is:
```r
plot(cars)
```
How can I make this be the preview image for the post?</div>
Being able to refer to easily refer to resources generated by the execution engines in our code is a good idea (I can imagine a similar feature being useful for the output of a `dot` or `mermaid` cell, or some arbitrary user shortcode) | {
"assignee": "cscheid",
"comments": 9,
"created_at": "2022-09-06T17:48:51Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 2324,
"state": "open",
"title": "Use plot as blog post image",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2324"
} |
This is a good way to tame the path behavior of includes. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-06T16:02:21Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2320,
"state": "closed",
"title": "Includes should support absolute paths",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2320"
} |
### Bug description
If I have an R figure section with
```
```{r fig-xyz}
#| fig.cap: "Local Moran's I at $\alpha=0.005$"
plot(1)
```
(the closing back-quotes won't render) it errors with: `ERROR: SyntaxError: Unexpected token a in JSON at position 22` (not pointing to file/line). I would like to actually use that feature: with a single quote and a math equation. If I remove the math $ symbols, things work.
This is with RStudio 2022.07.1 Build 554, quarto command line 1.0.38. Ubuntu 20.04 (or 22.04, don't know).
[xx.qmd.zip](https://github.com/quarto-dev/quarto-cli/files/9498511/xx.qmd.zip)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2022-09-06T15:42:34Z",
"creator": "edzer",
"is_pull_request": false,
"labels": [
"enhancement",
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2317,
"state": "closed",
"title": "single quote + math equation in fig.cap, unhelpful error message",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2317"
} |
### Bug description
I have been unable to render my document in versions 1.1.179 or 1.1.189. I am on Windows 10 using VS Code but I have replicated the issue in CLI with Powershell and CMD. I have seen the following error:
```powershell
└─$ quarto render .\test.qmd --to html
ERROR: NotFound: The system cannot find the path specified. (os error 3)
```
The contents of the file are simple:
---
title: Just a test
author: Me
date: September 6, 2022
---
# My first header
Lorem ipsum.... you know the drill.
```{python}
print(f"My Python Cell")
```
If I run the render on my local `C:\` drive, it runs successfully. But, if I run on a mapped NFS drive, e.g. `Z:\` -> `\\someserver\somefolder\`, then I get the error. If I include the `--execute-debug` flag I get:
```powershell
└─$ quarto render .\test.qmd --to html --execute-debug
- Connecting to kernel
ERROR: NotFound: The system cannot find the path specified. (os error 3)
```
Any thoughts on what is happening? The `--debug` flags don't add any information.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 11,
"created_at": "2022-09-06T15:36:50Z",
"creator": "white-c",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"windows",
"file-systems"
],
"locked": false,
"milestone": "v1.3",
"number": 2316,
"state": "closed",
"title": "NotFound Error when rendering Python or Julia cells on an NFS mount ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2316"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2312
<div type='discussions-op-text'>
<sup>Originally posted by **plessl** September 6, 2022</sup>
Hi Quarto community.
I recently discovered Quarto and I'm very impressed by this wonderful software.
I'm currently preparing a companion site to a lecture using Quarto where it would be helpful to keep code examples in files and include the contents in an HTML code cell in order to avoid code duplication (and to work around some limitations in Quarto, Juypter and Julia).
I would like to write code like this:
````
```julia
{{< include example.jl >}}
```
````
Unfortunately, this doesn't work. Instead of the contents of `example.jl` Quarto treats `{{< include example.jl >}}` like a line of Julia code and prints it. Is this a bug? Or does the include need to be escaped somehow?
Thanks,
Christian
</div> | {
"assignee": "cscheid",
"comments": 8,
"created_at": "2022-09-06T12:56:39Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2314,
"state": "closed",
"title": "Include file contents in code block is not working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2314"
} |
### Bug description
I have simple Quarto document with one R and one Python chunk. I want to access R variables in the python chunk via reticulate (`reticulate::repl_python()`) which works fine when I work with the document in RStudio.
```
---
title: "Example"
format: html
engine: knitr
---
```
```{r}
# r chunk
library(reticulate)
data(cars)
```
```{python}
# python chunk
car_df=r.cars
car_df
```
However, when I am using VSCode it doesn't work anymore. When I execute the python chunk, a Python REPL is started that has nothing to do with the R Session. Thus, I get a NameError in the python chunk because `name 'r' is not defined`.
Am I using the wrong settings in VSCode? Why isn't the Python REPL started via `reticulate::repl_python()` as it is in RStudio? Funnily, if I knit the Quarto document in VSCode everything is working fine. It might be important that I am working over an SSH connection in VSCode.
I know that I could simply type in the R console `reticulate::repl_python()`, but it would be much more convenient if VSCode would "automatically" use the correct repl.
### Version Info
RStudio Server Version: 2022.07.1+554
VSCode Version: Version: 1.71.0
OS: Ubuntu 20.04.5 LTS (Focal Fossa)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 7,
"created_at": "2022-09-06T12:54:42Z",
"creator": "schae211",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2313,
"state": "open",
"title": "Using reticulate in VSCode when dynamically executing quarto document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2313"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2308
<div type='discussions-op-text'>
<sup>Originally posted by **emmansh** September 5, 2022</sup>
I'm trying to set up a quarto website with some SQL code chunks. Trying to reproduce some DB code from [R4DS book](https://r4ds.hadley.nz/databases.html#in-this-book) fails with quarto website.
<pre>
# index.qmd
```{r}
library(DBI)
library(duckdb)
```
```{r}
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = "duckdb")
dbWriteTable(con, "mpg", ggplot2::mpg)
```
```{sql, connection=con}
SELECT manufacturer, displ, cty
FROM mpg
ORDER BY manufacturer, displ DESC
```
</pre>
Then in terminal
```shell
quarto preview
```
I get the following print:
```
Preparing to preview
[1/1] index.qmd
processing file: index.qmd
|......... | 12%
ordinary text without R code
|.................. | 25%
label: unnamed-chunk-1
|.......................... | 38%
ordinary text without R code
|................................... | 50%
label: unnamed-chunk-2
|............................................ | 62%
ordinary text without R code
|.................................................... | 75%
label: unnamed-chunk-3
|............................................................. | 88%
ordinary text without R code
|......................................................................| 100%
label: unnamed-chunk-4 (with options)
List of 2
$ connection:Formal class 'duckdb_connection' [package "duckdb"] with 5 slots
.. ..@ conn_ref :<externalptr>
.. ..@ driver :Formal class 'duckdb_driver' [package "duckdb"] with 3 slots
.. .. .. ..@ database_ref:<externalptr>
.. .. .. ..@ dbdir : chr "duckdb"
.. .. .. ..@ read_only : logi FALSE
.. ..@ debug : logi FALSE
.. ..@ timezone_out : chr "UTC"
.. ..@ tz_out_convert: chr "with"
$ engine : chr "sql"
Quitting from lines 26-29 (index.qmd)
Error: No method for S4 class:duckdb_connection
Execution halted
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
```
Why can't I use `duckdb()` for establishing a connection and using an SQL code chunk in quarto website? It's worth noting that same code works in regular, non-website, `.rmd` file.</div> | {
"assignee": "cderv",
"comments": 14,
"created_at": "2022-09-06T09:11:45Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2310,
"state": "closed",
"title": "`Error: No method for S4 class:duckdb_connection` when incorporating SQL chunks with quarto website",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2310"
} |
I am not sure if it's the right place to ask this question. Many issues are about bugs. But any comment is appreciated.
In quarto, the qmd file may contain bit of latex syntax witch can be treated later by pandoc itself or additional filters. The function of filter is introduced by [quarto online guide](https://quarto.org/docs/extensions/filters.html). So my curiosity is could quarto specify input format like this in pandoc
`pandoc -read=latex test.md -o test.docx` for rendering latex (if not specified, the pandoc or filter will nor render it, and the latex syntax is missed in the final docx file). I met something about format like this
```
format:
html:
theme: cosmo
pdf:
documentclass: scrreport
epub:
cover-image: cover.png
```
in __quarto.yml_ but I thought it is for output. Am I right? | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-06T03:42:11Z",
"creator": "Serenade600",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2309,
"state": "closed",
"title": "Can quarto specify input format like --read= in pandoc?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2309"
} |
## Edited
All images in <https://quarto.org/docs/authoring/figures.html#figure-basics> highlight center-aligne caption while the current design is to left-align captions as mentioned in the documentation.
Images should be updated to be consistent with the current design, thus exhibit caption left-aligned.
## Original issue
<details><summary>See the original issue content</summary>
_Initially discussed in #2304._
It appears for `html` format, `quarto-figure-center` css rule has no effect on caption, _i.e._, it's not possible to reproduce <https://quarto.org/docs/authoring/figures.html#figure-basics> as of Quarto `v1.1.189` (did not try v1.2 pre-release).
<img width="1484" alt="image" src="https://user-images.githubusercontent.com/8896044/188498861-a1a8fa71-414f-45e8-ba36-22874eb6aa68.png">
From the scss rules file: https://github.com/quarto-dev/quarto-cli/blob/main/src/resources/formats/html/_quarto-rules.scss#L93-L101
It we change the inheritance rule, then the expected results can be obtained.
````
---
title: "Untitled"
format: html
---
```{=html}
<style>
.quarto-figure-center > figure {
text-align: center;
}
</style>
```
## Title
{width="50px"}
````
<img width="1624" alt="image" src="https://user-images.githubusercontent.com/8896044/188498927-abaa5bd1-967e-4912-909e-6a8aaf3ebefa.png">
While for `revealjs` format, since the caption is not associated with the image, it is not centered (does not have the `quarto-figure-center` treatment).
It would be nice, to have a consistent behaviour between `html` and `revealjs` for captioned figures.
```html
<section id="title" class="slide level2 present" style="display: block;">
<h2>Title</h2>
<img width="50" class="r-stretch quarto-figure-center" src="https://upload.wikimedia.org/wikipedia/commons/thumb/1/1a/Elephant_Diversity.jpg/1920px-Elephant_Diversity.jpg" data-lazy-loaded="" style="height: 551px; width: 698.758px;"><p class="caption">Elephant</p>
</section>
```
</details> | {
"assignee": "cwickham",
"comments": 6,
"created_at": "2022-09-05T18:18:50Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 2306,
"state": "open",
"title": "Update images in documentation to highlight left-aligned captions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2306"
} |
### Bug description
It could be useful to add one alias for all slides output in our the format detection utility function (https://quarto.org/docs/extensions/lua.html#format-detection) so that it is easy to target slides in a Lua filter only for slides.
Example: Removing Pause syntax
````lua
Para = function(e)
if (not quarto.doc.isFormat("revealjs") or not quarto.doc.isFormat("beamer") or not quarto.doc.isFormat("pptx")) then
if (e == pandoc.Para '. . .') then
return {}
end
end
return nil
end
```` | {
"assignee": "cderv",
"comments": 0,
"created_at": "2022-09-05T15:40:38Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2305,
"state": "open",
"title": "Add an alias to target all slides format in `quarto.doc.isFormat()`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2305"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2300
<div type='discussions-op-text'>
<sup>Originally posted by **mlarocca-git** September 5, 2022</sup>
I have been a Rmarkdown user for a long time. Recently I switched all Rmarkdown projects to Quarto.
I have a minor problem and haven't found any solution in previous discussions.
In my reavealjs slides, I use a lot the pause within slides by inserting three dots separated by spaces.
There is no problem when I render a qmd file to HTML format. The "pause operator" does not appear in the final HTML. However, when I render a qmd file to a pdf via latex, the pause operator (the three dots) appears everywhere in the final pdf.
Is there any way to instruct Pandoc to ignore the string ". . ." when producing the final pdf?
Thank you so much for your help.
</div> | {
"assignee": null,
"comments": 6,
"created_at": "2022-09-05T14:36:33Z",
"creator": "allenmanning",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2302,
"state": "closed",
"title": "Pause within slides in revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2302"
} |
### Bug description
Citations in captions provided inside R chunks are properly resolved for **figures** (which is amazing, many thanks), but not for gt **tables**.
Example:
````
---
format: html
references:
- id: author:2015
author:
- family: Author
given: Ann
edition: '2'
issued:
- year: 2015
language: en-US
publisher: A publisher
publisher-place: A place
title: A book
type: book
---
```{r}
#| label: fig-airquality
#| fig-cap: 'Temperature and ozone level [Source: @author:2015, 67].'
#| warning: false
#| echo: false
library(ggplot2)
ggplot(airquality, aes(Temp, Ozone)) + geom_point()
```
```{r}
#| label: tbl-gt
#| tbl-cap: 'A toy example tibble for testing with gt [Source: @author:2015, 77].'
#| warning: false
#| echo: false
library(gt)
library(tidyverse)
exibble %>%
gt()
```
| Col1 | Col2 | Col3 |
|------|------|------|
| A | B | C |
| E | F | G |
| A | G | G |
: My Caption [Source: @author:2015, 87]. {#tbl-letters}
````
Output (just the caption lines, as visible in a browser window), note the unresolved citation in Table 1:
> Figure 1: Temperature and ozone level (Source: Author 2015, 67).
> Table 1: A toy example tibble for testing with gt [Source: @author:2015, 77]
> Table 2: My Caption (Source: Author 2015, 87).
The same results are seen when trying flextable or huxtable. kable, however, works as expected.
Given that quarto seems to be [committed to supporting all popular table packages, in particular gt](https://github.com/quarto-dev/quarto-cli/issues/1556#issuecomment-1219621832), it would be great if quarto could be made to support citations in gt table captions as well as it does for figure captions. Making this work for flextable and huxtable would of course be highly welcome as well.
---
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 11_6_8) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
quarto -v
1.1.179
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-09-05T11:54:22Z",
"creator": "njbart",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2297,
"state": "open",
"title": "Citations in gt table captions not resolved",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2297"
} |
@jph00 reports:
I just tried it with the latest quarto, and in a directory with just a single ipynb and a minimal _quarto.yml I got this error:
```
$ RUST_BACKTRACE=full quarto render
assertion failed [block != nullptr]: BasicBlock requested for unrecognized address
(BuilderBase.h:550 block_for_offset)
thread 'main' panicked at 'failed to get deno exit code', src/main.rs:101:37
stack backtrace:
0: 0x100d6bb24 - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::h85521558a183f368
1: 0x100d82b8b - core::fmt::write::h01631fae0d2b98bc
2: 0x100d68d78 - std::io::Write::write_fmt::h675dde99a2999169
3: 0x100d6d0ad - std::panicking::default_hook::{{closure}}::h5e5df492d229fd65
4: 0x100d6ce04 - std::panicking::default_hook::h18647b59f1a84ee2
5: 0x100d6d5e8 - std::panicking::rust_panic_with_hook::hd9ead35a68ccc55e
6: 0x100d6d523 - std::panicking::begin_panic_handler::{{closure}}::h6fca91c5e1dc2f30
7: 0x100d6bfa7 - std::sys_common::backtrace::__rust_end_short_backtrace::h4ff3025d9a0a0490
8: 0x100d6d1fa - _rust_begin_unwind
9: 0x100d89843 - core::panicking::panic_fmt::h3d9f795ee387ef8d
10: 0x100d81d7b - core::panicking::panic_display::h57aa0e5ca0e6a595
11: 0x100d81d2c - core::panicking::panic_str::h13f91ca11a013f3e
12: 0x100d896d9 - core::option::expect_failed::hed5528a77aee7737
13: 0x100d47709 - quarto::main::hcf1aaa9959ffbc6d
14: 0x100d480b6 - std::sys_common::backtrace::__rust_begin_short_backtrace::h9f94d688d5885adb
15: 0x100d4812c - std::rt::lang_start::{{closure}}::h58a78b66d00be7f2
16: 0x100d6504e - std::rt::lang_start_internal::h3fd5cff071397f19
17: 0x100d48019 - _main
```
Here's the `_quarto.yml`
```yaml
project:
type: website
website:
title: "testquarto"
description: "Experimenting with quarto"
sidebar:
contents:
- index.ipynb
```
| {
"assignee": "jjallaire",
"comments": 7,
"created_at": "2022-09-05T10:46:29Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2296,
"state": "closed",
"title": "rust launcher: crash on retrieving exit code from deno",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2296"
} |
### Bug description
````markdown
---
format: pdf
keep-md: true
keep-tex: true
---
```{r}
#| label: tbl-iris
#| tbl-cap: "Iris Data"
library(knitr)
kable(head(iris), format = "latex", table.envir = "table", position = "h!")
```
````
**knitr** will generate table in LaTeX, with a specific table option, and Quarto will insert caption in the wrong place, as the option filed is not taken into account in our regex matching probably
````latex
\begin{table}
\caption{\label{tbl-iris}Iris Data }\tabularnewline
[h!]
\begin{tabular}{r|r|r|r|l}
\hline
Sepal.Length & Sepal.Width & Petal.Length & Petal.Width & Species\\
\hline
5.1 & 3.5 & 1.4 & 0.2 & setosa\\
\hline
4.9 & 3.0 & 1.4 & 0.2 & setosa\\
\hline
4.7 & 3.2 & 1.3 & 0.2 & setosa\\
\hline
4.6 & 3.1 & 1.5 & 0.2 & setosa\\
\hline
5.0 & 3.6 & 1.4 & 0.2 & setosa\\
\hline
5.4 & 3.9 & 1.7 & 0.4 & setosa\\
\hline
\end{tabular}
\end{table}
````
We fixed some issues like that in the past, and we probably missed some cases
First reported in https://github.com/quarto-dev/quarto-cli/discussions/2264#discussioncomment-3541972
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 0,
"created_at": "2022-09-05T09:00:20Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2295,
"state": "closed",
"title": "Table caption inserted in wrong place in LaTeX table",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2295"
} |
### Bug description
This report describes an issue with obtaining bibliographic data directly from Zotero, bypassing the need for exporting `.bib`, `.json`, or `.yaml` bibliographic data, by using the Zotero add-on [zotxt](https://github.com/egh/zotxt) and the associated pandoc filter [pandoc-zotxt.lua](https://github.com/odkr/pandoc-zotxt.lua/).
**Using Rmarkdown**, it is possible to knit/render files such as the following from within RStudio (provided Zotero is running, and an entry `@bard:2015introduction` does exist):
```
---
output:
html_document:
pandoc_args:
- '--lua-filter'
- pandoc-zotxt.lua
- '--citeproc'
---
Blah blah [@bard:2015introduction, 67].
```
Result:
> Blah blah (Bard 2015, 67).
> Bard, Kathryn A. 2015. *An Introduction to the Archaeology of Ancient Egypt.* 2nd ed. Hoboken, NJ: Wiley-Blackwell.
**Using quarto from the command line**, with this file (`test.qmd`)
```
---
format: html
---
Blah blah [@bard:2015introduction, 67].
```
and the command
```
quarto render test.qmd -L /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua -C
```
produces the exact same expected result.
(Note that I had to provide the full path to the filter here, but that seems to be a different issue.)
For **`qmd` from within RStudio**, one would expect to be able to achieve the same with appropriate settings in the YAML metadata block; however, this does not seem to be possible, as using `pandoc-args` (or `pandoc_args`) has no effect, and [does not seem to be supported anyway](https://github.com/quarto-dev/quarto-cli/discussions/630).
Example:
```
---
format:
html:
pandoc-args:
- '--lua-filter'
- /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
- '--citeproc'
---
Blah blah [@bard:2015introduction, 67].
```
Result:
> Blah blah [@bard:2015introduction, 67].
(i.e., citation not resolved)
Including `filters` and `citeproc: TRUE` in the header has no effect either:
```
---
filters:
- /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
citeproc: TRUE
format: html
---
Blah blah [@bard:2015introduction, 67].
```
Result:
> Blah blah [\@bard:2015introduction, 67].
(i.e., citation not resolved)
What does work is including the instruction to use a bibliography file (`dummy.json`) which includes only one (dummy) entry, different from `@bard:2015introduction`. This seems sufficient to trigger the activation of `citeproc`.
```
---
filters:
- /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
format: html
bibliography: dummy.json
---
Blah blah [@bard:2015introduction, 67].
```
Result: as expected (note that not even `citeproc: TRUE` is required here).
**Possible solutions:**
1. Allow the use of `citeproc` as a (pseudo-) filter (note that the the order of filters matters)
```
filters:
- /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
- citeproc
```
2. Include support for using `pandoc-args` (or `pandoc_args`) in a YAML metadata block.
3. Make the following work:
```
filters:
- /Users/nb/.local/share/pandoc/filters/pandoc-zotxt.lua
citeproc: TRUE
```
A problem I see here, though, is that in this particular case `pandoc-zotxt.lua` has to be run before `citeproc`, but there might be other filters that have to be run after `citeproc`, so the option to force a specific order of filters (and pseudo-filters) which would be possible with 1. and 2. might be best.
---
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 11_6_8) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
quarto -v
1.1.179
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 8,
"created_at": "2022-09-05T08:51:16Z",
"creator": "njbart",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2294,
"state": "closed",
"title": "citeproc settings in YAML metadata block: Problems when using pandoc-zotxt.lua filter",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2294"
} |
### Bug description
A simple quarto file with the following lines:
````qmd
---
title: "test"
format: html
editor: visual
---
+------------------------------------+-----------------------------------------------------+
| 读，再读，反复读 | 经验丰富的研究者通常有一份不断完善的 “文献目录”。大约五十页到一百页左右。这份文献目录集里集中了他们所在专业的核心参考文献，有了这份目录，他们才能非常熟悉自己所在专业的文献，当然，要制作这样一份目录，学生们首先要读足够多的书。|
+------------------------------------+-------------------------------------------------------+
| 写，再写，反复写 | |
| | - 写作是熟能生巧的一项技能：写得越多。写起来也就越容易。 |
| | - 在写作的时候应该以出版为目的，也就是要成文，这样做的好处之一首先是可以为将来的修订带来不少便利，其次是如果有人对你的研究感兴趣的话，你也有东西可以展示给他们看。|
| | - 不要扔掉你写过的东西。把它们编好日期并存放在一个“便携”文件夹里，这些材料对你来说可能会是很有用的。|
| | - 做修订通常比写新东西来得容易。 |
+------------------------------------+-------------------------------------------------------+
````
Quarto rendered as:
But with `rmarkdown::render()`:
RStudio version on Windows 11:
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-09-05T04:00:49Z",
"creator": "psychelzh",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2292,
"state": "closed",
"title": "Grid table with different row lengths are not properly rendered",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2292"
} |
I was hunting an error in one of my extensions today and it took me a very long time to understand what was going wrong. The error message I was getting was `ERROR: Source and destination cannot be the same.`
This was caused by a missing format ressource I had listed under `format-resources`. Would it be possible to have a clearer error when this happens? | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-04T19:57:15Z",
"creator": "Nenuial",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": null,
"number": 2291,
"state": "closed",
"title": "More informative error when format-resources isn't found",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2291"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2289
<div type='discussions-op-text'>
<sup>Originally posted by **andrewpbray** September 4, 2022</sup>
I have been setting `code-folding: true` for my html doc, but I find the "Code" text next to the toggle triangle to be somewhat distracting (this is for a doc where 95% of readers won't/shouldn't care about the code). I spotted that there's a `code-summary` option where you can pass it an alternative label like "Click here for code".
When I tried to leave it as an empty string I get:
```yaml
---
title: "Untitled"
format:
html:
code-fold: true
code-summary: ""
---
```
```
Error running filter /Applications/quarto/share/filters/quarto-post/quarto-post.lua:
...cations/quarto/share/filters/quarto-post/quarto-post.lua:1119: attempt to index a nil value (field 'integer index')
stack traceback:
...cations/quarto/share/filters/quarto-post/quarto-post.lua:2282: in function <...cations/quarto/share/filters/quarto-post/quarto-post.lua:2264>
```
`code-summary: " "` doesn't do it either - it gets rendered as:
<img width="117" alt="Screen Shot 2022-09-04 at 8 37 08 AM" src="https://user-images.githubusercontent.com/1627362/188321646-311d5a0b-cd84-4312-a3b1-644a86231515.png">
I don't have a good hold on how yaml field values are parsed, but this is surprising behavior since something like `title: ""` works ok.
</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-09-04T16:42:18Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2290,
"state": "closed",
"title": "Leaving code-summary empty",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2290"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2282
<div type='discussions-op-text'>
<sup>Originally posted by **produnis** September 4, 2022</sup>
Hi there,
I am creating a book, and I added a "description" in the _quarto.yaml file.
Now, the HTML file contains a META Descritpion entry, but, additionally, the text of that description is posted on top of every page of the book.
My question is: why is that, and is there a way to turn it off?</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-09-04T14:50:00Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2286,
"state": "closed",
"title": "Book description displayed on every page.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2286"
} |
When the `lang` is specified under a format, like:
```
format:
html:
lang: zh
```
We don't respect that lang when rendering a book (it must instead be at the root level).
See #251 | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-09-04T13:37:45Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 2285,
"state": "open",
"title": "`lang` provided under `format` key not respected when rendering books",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2285"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2283
<div type='discussions-op-text'>
<sup>Originally posted by **jhchou** September 4, 2022</sup>
Is there a way to specify `target="_blank` in `href`'s in YAML's, for example in `about.qmd` or the `navbar:` in `_quarto.yml`?
As mentioned here, it's possible in Markdown: [Is it possible to make all hrefs open in a new tab?](https://github.com/quarto-dev/quarto-web/discussions/354) as follows:
[some text](some-url){target="_blank"}
... but I haven't been able to find a way to do so in YAML hrefs.</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-04T13:14:32Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 2284,
"state": "closed",
"title": "Support `target` for NavItems (e.g. about page, navbar, Sidebar)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2284"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2278
<div type='discussions-op-text'>
<sup>Originally posted by **mavam** September 3, 2022</sup>
I'm outputting my qmd in GFM, which puts code and output adjacent to each other. I would like to wrap *only the code* in a `<details>` section:
I tried this:
<details><summary>Code</summary>
```{r}
data |> ggplot(..)
```
</details>
But this also puts the output (in this case, a plot) into the details section. I couldn't find an option for that in the [GFM docs](https://quarto.org/docs/reference/formats/markdown/gfm.html).
My hunch is that I need to write a filter, ~but wrangling the AST in Lua is a different ballpark.~ EDIT: I managed to write a filter, but it feels pretty hacky:
```lua
function CodeBlock(code_block)
if code_block.attributes["code-fold"] == "true" then
local open = "<details><summary>Code </summary>\n"
local close = "\n</details>"
local open_block = pandoc.RawBlock("html", open)
local close_block = pandoc.RawBlock("html", close)
return {open_block, code_block, close_block}
end
return code_block
end
```
Is that the right approach?
(NB: I'm aware that HTML output does this. But I need to output to GFM where there is no collapse option.)
</div> | {
"assignee": "jjallaire",
"comments": 4,
"created_at": "2022-09-03T23:17:41Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.2",
"number": 2279,
"state": "closed",
"title": "[FR] Extend `code-fold: true` to other formats such as `gfm`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2279"
} |
### Bug description
[Following pandoc's documentation](https://pandoc.org/MANUAL#on-all-slides-beamer-reveal.js-pptx), I have been using the following code in a qmd document I want to be rendered as a revealjs and where I want the title's slide having a specific background.
```qmd
---
title: "My Fancy title"
title-slide-attributes:
data-background-image: "https://upload.wikimedia.org/wikipedia/commons/archive/8/8c/20210225154040%21Folio-Quarto-Octavo_Compared.svg"
data-background-opacity: "0.40"
data-background-color: "#552D62"
format:
revealjs:
theme: serif
transition: slide
background-transition: fade
---
# Some fancy title
```
This code has been working in the past, with Quarto v 1.0.38, but I just updated to 1.1.179 and stopped working.
The error I get now is (either in RStudio and in VS Code):
```
ERROR: Validation of YAML front matter failed.
ERROR: In file slides.qmd
(line 11, columns 5--26) property name data-background-color is invalid
10: # data-background-size: contain
11: data-background-color: "#552D62"
~~~~~~~~~~~~~~~~~~~~~
12: data-background-opacity: "0.40"
ℹ The error happened in location title-slide-attributes:data-background-color.
ERROR: Render failed due to invalid YAML.
```
Also, vscode's warning me that `data-background-color`is not a valid property.
If I comment out the line with `data-background-color`the slides are rendered perfectly, but of course, they are not rendered as I'd like them to look like.
**My environment:**
* Quarto version: 1.1.179
* VSCodium: Version: 1.70.2
Release: 22230
Commit: 6c122d9b2d1af2c37bd55caad614321eb53b342f
Date: 2022-08-18T00:40:55.241Z
Electron: 18.3.5
Chromium: 100.0.4896.160
Node.js: 16.13.2
V8: 10.0.139.17-electron.0
OS: Darwin x64 21.6.0
* RStudio: 2022.07.1 Build 554
* OS: MacOS 12.5
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-09-03T16:06:39Z",
"creator": "ccamara",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2277,
"state": "closed",
"title": "`data-background-color` property stopped working in quarto 1.1.179",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2277"
} |
### Bug description
I am struggling to label multiple equations placed within `$$ \begin{align} ... \end{align} $$`.
This works flawlessly...
```
$$
\begin{align}
a &= 0+1 \\
b &= 2+3 \\
c &= 4+5
\end{align}
$$ {#eq-abc}
see @eq-abc.
```
...but neither of these work:
```
$$
\begin{align}
a &= 0+1 \label{eq:a} \\
b &= 2+3 \label{eq-c} \\
c &= 4+5 {#eq-d}
\end{align}
$$
```
I tried various other versions of Quarto and/or LaTeX syntax, but couldn't achieve the desired results: To have multiple numbered (and cross-referenceable) equations placed within an align-block.
Any suggestions would be greatly appreciated! And, it would be nice to have such an example included in the Equations sections of the Technical Writing documentation [here](https://quarto.org/docs/visual-editor/technical.html).
**Software:**
- Quarto version 1.1.168
- macOS Monterey version 12.2
- RStudio IDE version "Prairie Trillium" Release
(1db809b8, 2022-05-16) for macOS
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-09-03T09:26:30Z",
"creator": "HelenaLC",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2275,
"state": "open",
"title": "referencing equations inside `$$ \\begin{align}` environment",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2275"
} |
Hello, I am using quarto to build a blog. I have a problem. I need the URL address of each article. How can I solve it? I can only get the title of the article through meta, eg:`{{< meta date >}}`, but I can't find the data related to the URL address
| {
"assignee": null,
"comments": 3,
"created_at": "2022-09-03T02:52:44Z",
"creator": "zoushucai",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3381,
"state": "closed",
"title": "How to get the URL of a web page",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3381"
} |
### Bug description
Issue taken from [Stack Overflow](https://stackoverflow.com/questions/73548259/tabsets-not-rendering-datatables-properly-for-quarto-revealjs-presentation) and is reproducible on my system (macOS, latest) with Quarto `1.1.179`. Problem is that in later slides some of the DT tables aren't rendered (usually in tabs 2 and 3). Refreshing causes them to appear. Might be a variation of https://github.com/quarto-dev/quarto-cli/issues/1076.
````
---
title: "test"
format: revealjs
editor: visual
---
---
format:
revealjs
execute:
echo: false
message: false
---
```{r}
#| label: load-packages
#| include: false
library(tidyverse)
library(DT)
options(dplyr.summarise.inform = FALSE)
```
# Data prep
```{r echo=TRUE}
dat1 <- diamonds %>%
group_by(cut) %>%
summarize(n = n(), price = round(mean(price), 2))
dat2 <- diamonds %>%
group_by(carat) %>%
summarize(n = n(), price = round(mean(price), 2))
dat3 <- diamonds %>%
group_by(clarity) %>%
summarize(n = n(), price = round(mean(price), 2))
```
## Page 1
::: panel-tabset
### Tab 1
```{r}
#| label: tab-1-1
datatable(dat1)
```
### Tab 2
```{r}
#| label: tab-1-2
datatable(dat2)
```
### Tab 3
```{r}
#| label: tab-1-3
datatable(dat3)
```
:::
## Page 2
::: panel-tabset
### Tab 1
```{r}
#| label: tab-2-1
datatable(dat3)
```
### Tab 2
```{r}
#| label: tab-2-2
datatable(dat1)
```
### Tab 3
```{r}
#| label: tab-2-3
datatable(dat2)
```
:::
## Page 3
::: panel-tabset
### Tab 1
```{r}
#| label: tab-3-1
datatable(dat3)
```
### Tab 2
```{r}
#| label: tab-3-2
datatable(dat1)
```
### Tab 3
```{r}
#| label: tab-3-3
datatable(dat2)
```
:::
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 8,
"created_at": "2022-09-02T14:58:11Z",
"creator": "rich-iannone",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2271,
"state": "closed",
"title": "Issue rendering multiple DT tables in multiple `panel-tabset` (all appear reliably after refresh)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2271"
} |
### Bug description
Taken from [Community](https://community.rstudio.com/t/rstudioapi-askforpassword-function-in-quarto/146254) (2022-01-01):
When running RMD documents I use the rstudioapi::askForPassword function to push passwords to databases. This works both in interactive mode and when knitting.
However when using qmd, when I hit the "render" button in RStudio 2022.07.1 Build 554
I get the error
Quitting from lines 16-19 (test.qmd)
Error: RStudio not running
I'm not sure how to create a reprex since it is an issue with rendering an RMD, but I get the error just by adding the command rstudioapi::askForPassword("testing") to an R chunk inside the default qmd template that is created when you do file > new quarto document
Is it not possible to use the rstudioapi package when rendering a qmd?
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 3,
"created_at": "2022-09-02T13:22:44Z",
"creator": "rich-iannone",
"is_pull_request": false,
"labels": [
"bug",
"upstream"
],
"locked": false,
"milestone": "Future",
"number": 2269,
"state": "closed",
"title": "Cannot use `rstudioapi::askForPassword()`; works in .Rmd",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2269"
} |
### Bug description
When I'm trying to save a self-contained HTML file to a specific file, it appears that it doesn't contain any CSS. Everything is file when `output-file` is not specified:
without output-file in the YAML header:
with output-file:
I'm using R via Rstudio on Windows:
```
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
```
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-09-02T09:39:01Z",
"creator": "davidbudzynski",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2266,
"state": "closed",
"title": "Self-contained feature does not include CSS when output-file is specified",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2266"
} |
Beamer reference from [here](https://quarto.org/docs/reference/formats/presentations/beamer.html) does not list the `theme` format option, but it does exist, i.e. the following works:
```
format:
beamer:
theme: Madrid
```
The reference should be updated to include `theme`. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-01T21:31:41Z",
"creator": "nikcleju",
"is_pull_request": false,
"labels": [
"enhancement",
"yaml-validation"
],
"locked": false,
"milestone": "v1.3",
"number": 3377,
"state": "closed",
"title": "Beamer reference does not list `theme` format option",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3377"
} |
Looks like we're either blocked on pandoc here: https://github.com/jgm/pandoc/issues/8268, or we have to ask users to install Python2 via homebrew etc. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-09-01T17:44:11Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2259,
"state": "closed",
"title": "Python filters don't work on Monterey 12.3 and later",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2259"
} |
### Bug description
I'm working on some course materials where I would like to embed stan models in a quarto document but currently models that I can successfully compile interactively will fail when rendering the document. The issue appears to be that since quarto is an x86 executable it is causing confusion with stan / clang such that they attempt to build the model as x86 instead of arm64 causing an issue with the model's shared library object being loaded. The same issues do not occur when compiling the same document using RMarkdown or on a linux x86 machine.
A basic reprex is possible with the following document when rendered on an m1 machine,
````
---
title: "test"
format: html
---
```{r}
model = "
data {
int<lower=0> N;
vector[N] x;
vector[N] y;
}
parameters {
real a;
real b;
real<lower=0> sigma;
}
model {
y ~ normal(a + b * x, sigma);
}
"
N = 10
x = runif(N)
y = x + rnorm(N)
rstan::stan(model_code = model, data = list(N=N, x=x, y=y), chains=1)
```
````
which produces the following output when rendered on my M1 mac
````
processing file: test.qmd
|................................... | 50%
ordinary text without R code
|......................................................................| 100%
label: unnamed-chunk-1
Quitting from lines 9-30 (test.qmd)
Error in dyn.load(libLFile) :
unable to load shared object '/var/folders/ds/8sqz2v4d355btthn6r88kdc00000gn/T//RtmpU2OC1K/file153642d93e83d.so':
dlopen(/var/folders/ds/8sqz2v4d355btthn6r88kdc00000gn/T//RtmpU2OC1K/file153642d93e83d.so, 0x0006): tried: '/var/folders/ds/8sqz2v4d355btthn6r88kdc00000gn/T//RtmpU2OC1K/file153642d93e83d.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/var/folders/ds/8sqz2v4d355btthn6r88kdc00000gn/T//RtmpU2OC1K/file153642d93e83d.so' (no such file), '/var/folders/ds/8sqz2v4d355btthn6r88kdc00000gn/T//RtmpU2OC1K/file153642d93e83d.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/private/var/folders/ds/8sqz2v4d355btthn6r88kdc00000gn/T/RtmpU2OC1K/file153642d93e83d.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/private/var/folders/ds/8sqz2v4d355btthn6r88kdc00000gn/T/RtmpU2OC1K/file153642d93e83d.so' (
Calls: .main ... cxxfunctionplus -> <Anonymous> -> cxxfunction -> dyn.load
Quitting from lines 11-32 (test.qmd)
Error in sink(type = "output") : invalid connection
Calls: .main ... <Anonymous> -> stan_model -> cxxfunctionplus -> sink
Execution halted
*** caught segfault ***
address 0x61706d6f636e6920, cause 'invalid permissions'
Traceback:
1: getLoadedDLLs()
2: f %in% names(getLoadedDLLs())
3: (function (env) { if (f %in% names(getLoadedDLLs())) dyn.unload(libLFile) unlink(libLFile)})(<environment>)
An irrecoverable exception occurred. R is aborting now ...
````
My hope is that this is fixable via overriding the appropriate compiler flags when invoking the R session / knitr.
This is occurring with quarto v1.1.167 and v1.2.15.
<details>
<summary>Session Info</summary>
````
> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os macOS Ventura 13.0
system aarch64, darwin21.5.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2022-09-01
rstudio 2022.07.1+554 Spotted Wakerobin (desktop)
pandoc 2.19.2 @ /opt/homebrew/bin/ (via rmarkdown)
─ Packages ──────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.1)
callr 3.7.2 2022-08-22 [1] CRAN (R 4.2.1)
cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.1)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.1)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.1)
crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.1)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.1)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.1)
dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.1)
evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.1)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1)
ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.2.1)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.2.1)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
inline 0.3.19 2021-05-31 [1] CRAN (R 4.2.1)
knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.1)
loo 2.5.1 2022-03-24 [1] CRAN (R 4.2.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.1)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.1)
processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.1)
ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.1)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.1)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.2.1)
rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.1)
rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.1)
rstan * 2.21.5 2022-04-11 [1] CRAN (R 4.2.1)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
StanHeaders * 2.21.0-7 2020-12-17 [1] CRAN (R 4.2.1)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)
vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.1)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
xfun 0.32 2022-08-10 [1] CRAN (R 4.2.1)
[1] /Users/rundel/Library/R/arm64/4.2/library
[2] /opt/homebrew/Cellar/r/4.2.1_2/lib/R/library
─────────────────────────────────────────────────────────────────────────────────
````
</details>
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 11,
"created_at": "2022-09-01T16:48:28Z",
"creator": "rundel",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.2",
"number": 2258,
"state": "closed",
"title": "quarto + stan + m1 compilation issue",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2258"
} |
it is - in principle - possible to test different versions with the [Windows Sandbox (& winget)](https://github.com/microsoft/winget-pkgs/blob/master/doc/tools/SandboxTest.md). I say "in principle" because it does not seem to work for quarto at the moment. `quarto -V` or `quarto check` don't show any output in the Sandbox. I am not sure whether this is a due to the Sandbox or due to Quarto. In general I think this is pretty powerful which is why I'd like to see [full Sandbox support for winget](https://github.com/microsoft/winget-cli/issues/2081) one day (Feel free to upvote 😉).
_Originally posted by @dpprdan in https://github.com/quarto-dev/quarto-cli/issues/1977#issuecomment-1234449649_ | {
"assignee": null,
"comments": 12,
"created_at": "2022-09-01T16:00:52Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.2",
"number": 2255,
"state": "closed",
"title": "Running Quarto in Windows Sandbox does not work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2255"
} |
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-09-01T14:55:19Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"pandoc-lua"
],
"locked": false,
"milestone": "Future",
"number": 2254,
"state": "closed",
"title": "`quarto.utils.dump` doesn't work with PANDOC_STATE",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2254"
} |
|
We get this on the latest IPython:
```
/var/folders/nm/m64n9_z9307305n0xtzpp54m0000gn/T/ipykernel_5300/1749505576.py:69: DeprecationWarning: Importing display from IPython.core.display is deprecated since IPython 7.14, please import from IPython display
from IPython.core.display import display, HTML
``` | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-01T14:36:43Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": null,
"number": 2253,
"state": "closed",
"title": "Deprecation message on IPython 7.14",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2253"
} |
### Bug description
```md
## Example
I'm going to pull in some dates calculated after this markdown block with Observable.
This works fine:
* Begin date: ${the_dates[0]}
* End date ${the_dates[1]}
So does this:
**${the_dates[1]}**
But this does **not** work!
The range is between **${the_dates[0]}** and **${the_dates[1]}**.
Yet this does!
The range is between **${the_dates[1]}** and ${the_dates[1]}.
```
Here is the python block that exists in the qmd file below all of this:
```{python}
import datetime
begin_date = datetime.datetime(2022,1,1).strftime("%B %-d, %Y")
end_date = datetime.datetime(2022,1,30).strftime("%B %-d, %Y")
ojs_define(the_dates = [begin_date,end_date])
```
This is running on OS X on a Mac Mini (m1) with Quarto 1.1.168.
It wants to me attach a file but if I drop over a .qmd file it says it's not supported. 😔 I made a [minimal repo here](https://github.com/astrowonk/quarto_bug) and attached a screenshot.
<img width="1058" alt="Screen Shot 2022-09-01 at 9 23 16 AM" src="https://user-images.githubusercontent.com/13702392/187924679-9f7bf192-4115-494c-9bb0-3b5346ed8a36.png">
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 10,
"created_at": "2022-09-01T13:23:25Z",
"creator": "astrowonk",
"is_pull_request": false,
"labels": [
"bug",
"wontfix"
],
"locked": false,
"milestone": "v1.3",
"number": 2252,
"state": "closed",
"title": "Markdown formatting around observable inline variables renders incorrectly.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2252"
} |
### Bug description
# repex
**.qmd:**
````
```{r}
url1 <- "https://www.haustier-news.de/welpen/wp-content/uploads/2020/09/pomeranian.jpg"
url2 <- "https://www.allthingsdogs.com/wp-content/uploads/2020/01/White-Pomeranian-Feature-678x381.jpg"
```
# this works
```{r}
#| label: a-pomeranian
#| out-width: 50%
knitr::include_graphics(url1)
```
```{r}
#| label: another-pomeranian
#| out-width: 25%
knitr::include_graphics(url1)
```
# this doesn't
```{r}
#| label: two-pomeranians
#| fig-show: hold
#| out-width: 25%
#| layout-nrow: 1
knitr::include_graphics(url1)
knitr::include_graphics(url2)
```
````
**output:**
# software
- Quarto version 1.1.168
- macOS Monterey version 12.2
- RStudio IDE version "Prairie Trillium" Release
(1db809b8, 2022-05-16) for macOS
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 9,
"created_at": "2022-09-01T12:51:34Z",
"creator": "HelenaLC",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2251,
"state": "open",
"title": "`#| out/fig-width:` ignored when specifying `#| layout-nrow/col:`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2251"
} |
I ran into this problem while deploying a quarto website to Rstudio Connect, but it may be useful for any site that's rendered with a cron job. Basically my site relies on long-running computation that I only want to render on Rstudio Connect The behaviour I'm after is:
1) Document uses frozen output when `quarto render` is run locally
2) Document runs the computation when deployed to Rstudio Connect
3) Document runs the computation when re-rendered on a schedule by RSC
I tried to do this with
```
execute:
freeeze: !expr Sys.getenv("R_CONFIG_ACTIVE" != "rsconnect")
```
And while that seems to work for a single html file it fails for a full site. It seems like there should be a cleaner interface for these types of config options which wasn't R-specific. For example there could be a config file which allowed the user to define YAML options on Rstudio Connect, Github actions, or when an environment variable was present.
| {
"assignee": null,
"comments": 11,
"created_at": "2022-09-01T12:48:49Z",
"creator": "GShotwell",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.2",
"number": 2250,
"state": "closed",
"title": "Config-based freezing",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2250"
} |
Just opening this to track idea from https://github.com/quarto-dev/quarto-cli/discussions/2230
Maybe we could add a feature to add a `quarto.utils.input_files()` (or similar) to easily access the source `.qmd` from a Lua filter.
Could be useful in certain case, and `PANDOC_STATE.input_files` can probably help for that.
Let's see if some 👍 are added by users developing with Lua. | {
"assignee": "cscheid",
"comments": 21,
"created_at": "2022-09-01T12:34:30Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"pandoc-lua"
],
"locked": false,
"milestone": "v1.3",
"number": 2249,
"state": "closed",
"title": "[FR] New Lua utility function to access qmd input filename",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2249"
} |
### Bug description
using the element below in _quarto.yml
```
format:
html:
theme:
dark: darkly
light: flatly
```
the page shows in dark mode per default, but if toggled to light mode, the site goes back to dark mode when navigating to a different page.
(This does not happen if light mode is the default)
I tested safari and firefox on OSX
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-09-01T10:40:22Z",
"creator": "jcolomb",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2248,
"state": "closed",
"title": "website: dark mode as default: toggle to light mode not kept between pages",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2248"
} |
### Bug description
**current behavior:**
- `#| fig-cap-location: margin` has no effect in code chunks that render multiple plots
**expected/desired behavior:**
- the main caption is placed in the margin
- sub-captions (a)-(z) are placed in the margin, underneath the main caption
- alternatively, these stay in the document by default, but there is/are separate chunk option(s) to control their placement
# repex
**.qmd:**
````
```{r}
#| label: fig-histograms-3
#| fig-cap-location: margin
#| fig-cap: "this works"
#| fig-width: 4
#| fig-height: 3
hist(rnorm(100))
```
```{r}
#| label: fig-histograms-4
#| fig-cap-location: margin
#| fig-cap: "this should be in the margin"
#| fig-subcap:
#| - ""
#| - ""
#| fig-show: hold
#| fig-width: 4
#| fig-height: 3
#| layout-nrow: 1
hist(runif(100))
hist(rnorm(100))
```
````
**output:**
# software
- Quarto version 1.1.168
- macOS Monterey version 12.2
- RStudio IDE version "Prairie Trillium" Release
(1db809b8, 2022-05-16) for macOS
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-09-01T10:17:47Z",
"creator": "HelenaLC",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2247,
"state": "closed",
"title": "`#| fig-cap-location:` is ignored by multi-plot code chunks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2247"
} |
### Bug description
# summary
**current behavior:**
- a code chunk that renders multiple plots with `#| fig-cap:` set duplicates the caption
- consequently, the figure counter is incremented twice
**expected/desired behavior:**
- sub-captions are optional: not specifying `#| fig-subcap:` gives a main caption only, without sub-panels being labeled (a)-(z)
- alternatively, there's a chunk option to mark figures as not/having labeled sub-panels
- an incorrect number of `#| fig-subcap:` items gives an error
- in either case, the figure counter is incremented once only (since there's one `#| fig-cap:` that can be cross-referenced)
# repex
**.qmd:**
````
```{r}
#| label: fig-histograms-1
#| fig-cap: "this caption is duplicated"
#| fig-show: hold
#| fig-width: 4
#| fig-height: 3
#| layout-nrow: 1
hist(runif(100))
hist(rnorm(100))
```
```{r}
#| label: fig-histograms-2
#| fig-cap: "this caption is unique"
#| fig-subcap:
#| - ""
#| - ""
#| fig-show: hold
#| fig-width: 4
#| fig-height: 3
#| layout-nrow: 1
hist(runif(100))
hist(rnorm(100))
```
````
**output:**
# software
- Quarto version 1.1.168
- macOS Monterey version 12.2
- RStudio IDE version "Prairie Trillium" Release
(1db809b8, 2022-05-16) for macOS
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-09-01T10:11:32Z",
"creator": "HelenaLC",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2246,
"state": "open",
"title": "Float crossrefs with unlabeled subfloats",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2246"
} |
### Bug description
Hi Guys
Everytime I try to render a Quarto documento to PDF I got an error about LaTeX and xelatex, could you help me with that?
Working with Windows 10, R 4.2.1, RStudio 2022.07.1
This is my yaml header
```
---
title: Bar Charts - R
date: today
description: El presente documento muestra como crear diagramas de barras (Bar Charts) en el lenguaje de programación R haciendo uso de la función barplot(), así como de los paquetes (packages) ggplot2 y lattice.
author:
name: Renzo Cácerers Rossi
url: https://www.youtube.com/c/RenzoCaceresRossi
affiliation: Rossi Corporation
affiliation-url: https://hablamosr.blogspot.com/
title-block-banner: "#808080"
format:
pdf:
theme: journal
toc: true
css: "style_003.css"
code-fold: true
code-tools: true
bibliography: biblio_003.bib
csl: apa.csl
link-citations: yes
number-sections: true
lang: Es-es
prefer-html: true
---
```
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2022-09-01T04:21:18Z",
"creator": "lightbluetitan",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2245,
"state": "open",
"title": "Can't render Quarto to PDF",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2245"
} |
### Bug description
Admittedly complicated notebooks not rendering correctly.
The image below shows part of the render of
https://gitlab.com/ea42gh/elementary-linear-algebra/-/blob/master/notebooks/04_MatrixAlgebra.ipynb
The directory contains a number of notebooks that all fail...
os: windows 11
quarto 1.1.113
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-31T22:00:30Z",
"creator": "ea42gh",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2243,
"state": "closed",
"title": "Jupiter notebook to html render problems",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2243"
} |
### Bug description
When using the YAML options `code-block-bg` and `code-block-border-left`, I obtain different behavior in HTML and PDF. The HTML version has the expected behavior, while the PDF does not.
## Code
### HTML Document
````
---
title: "test_html"
format:
html:
code-block-bg: "#f3f3f3"
code-block-border-left: "#31BAE9"
---
```{r}
1+2
```
````
#### Output
<img width="859" alt="Screen Shot 2022-08-31 at 13 53 26" src="https://user-images.githubusercontent.com/25734232/187759802-c9118469-9e1b-40c3-a1bf-748621e1071b.png">
### PDF Document
````
---
title: "test_pdf"
format:
pdf:
code-block-bg: "#f3f3f3"
code-block-border-left: "#31BAE9"
---
```{r}
1+2
```
````
#### Output
<img width="825" alt="Screen Shot 2022-08-31 at 13 54 15" src="https://user-images.githubusercontent.com/25734232/187759921-01b1310d-c7b3-4d8b-99bd-5a30b4ec797a.png">
## System Info
```
❯ quarto -v
1.1.168
```
RStudio: 2022.07.1 Build 554
MacOS Monterey 12.5.1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-08-31T18:56:28Z",
"creator": "maxdrohde",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2242,
"state": "closed",
"title": "Different code block color behavior in HTML and PDF output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2242"
} |
In order to have numbered callouts (e.g., for cross-referenceable exercises and solutions), I have attempted to
- set callout captions to be empty via the *_quarto.yml* file
- use "#exr-" (or similar) as headers in the callouts
with the somewhat unexpected result that
- printed names (here, "Exercise") are rendered twice
- the corresponding counted is incremented twice
I am not sure whether this is a bug per se, but any suggestions how to achieve/fix this would be greatly appreciated!
**_quarto.yml:**
```
format: html
language:
callout-note-caption: ""
```
**.qmd:**
```
::: {.callout-note #exr-one}
text
:::
See @exr-one.
```
**output:**
- This works, but isn't ideal:
```
::: {.callout-note}
::: {#exr-two}
text
:::
:::
See @exr-two.
```
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-31T17:58:27Z",
"creator": "HelenaLC",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2241,
"state": "open",
"title": "unexpected behavior in callouts using `#xxx-` label as header",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2241"
} |
We would like to place various contents inside collapsable callouts. Often, these include margin contents (e.g., notes via `[...]{.aside}`, figures, etc.). At the moments,
1. callouts are expanded to full page width
2. the collapse option is broken
Ideally, we would like
- margin-content to be placed in the margin next to the callout,
but without the box being expanded
- collapsing the callout to hide its contents (including what's in the margin)
**.qmd:**
````
::: {.callout-warning}
a margin[comment]{.aside}
:::
this is where the body begins
::: {.callout-warning collapse="false"}
```{r}
#| fig-cap: "histogram"
#| column: margin
hist(rnorm(100))
```
:::
````
**output:**
| {
"assignee": null,
"comments": 0,
"created_at": "2022-08-31T17:53:32Z",
"creator": "HelenaLC",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.2",
"number": 2240,
"state": "closed",
"title": "margin content expands callouts to full page width",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2240"
} |
In order to obtain numbered callouts (e.g., for cross-referenceable exercises and solutions), I have attempted to
- set callout captions to be empty via `callout-x-caption: ""`
- use `#exr-` (or similar) to get numbered captions instead
with the following unexpected outcome:
1. The printed name (here, "Exercise") is printed twice; and,
2. The corresponding counter is incremented twice.
I am not sure whether our not this is a bug/issue per se, but any suggestions would be greatly appreciated!
## minimal reproducible example:
- **_quarto.yml:**
```
format: html
language:
callout-note-caption: ""
```
- **.qmd:**
```
::: {.callout-note #exr-one}
text
:::
See @exr-one.
```
- **output:**
- This works, but is not ideal:
```
::: {.callout-note}
::: {#exr-two}
text
:::
:::
```
 | {
"assignee": null,
"comments": 3,
"created_at": "2022-08-31T17:22:43Z",
"creator": "HelenaLC",
"is_pull_request": false,
"labels": [
"crossref"
],
"locked": false,
"milestone": "v1.2",
"number": 2239,
"state": "closed",
"title": "unexpected behavior with callout using `#xxx-` label as header",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2239"
} |
https://github.com/quarto-dev/quarto-cli/blob/main/package/src/common/archive-binary-dependencies.ts#L113-L123
This needs to fail on a bad URL, otherwise we archive a bad dependency. | {
"assignee": "jjallaire",
"comments": 0,
"created_at": "2022-08-31T17:22:34Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2238,
"state": "closed",
"title": "archive-binary-dependencies needs to check for response status",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2238"
} |
### Bug description
While there are no partials in the revealjs pandoc template directory, there *seems* to be some support for them. In particular, if you try to specify a template partial in the document YAML header, such as:
````yaml
format:
revealjs:
template-partials:
- my-partial.html
````
The error that is thrown is:
```
ERROR: The format 'revealjs' only supports the following partials:
metadata.html
title-block.html
toc.html
```
Suggesting that there was at least a thought at some point to support those template partials. However, `template.revealjs` does not support those partials.
BUT, if I copy over `template.revealjs` and edit it to have support for a title block partial like so:
````html
$if(title)$
$title-block.html()$
$endif$
````
And set up my YAML header with:
````yaml
format:
revealjs:
template: modified-template.revealjs
template-partials:
- title-block.html
````
Then it all works as expected and my custom title block is substituted into the main template.
Is there any plan to make this the default behavior?
(FWIW, I'm trying to do some different title page layouts using grid/flex and while I **can** manage it using some ugly javascript munging, it would be a lot easier and cleaner to just be able to sub in a new title template.)
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-08-31T16:27:06Z",
"creator": "ryanraaum",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2236,
"state": "closed",
"title": "Support for revealjs template partials?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2236"
} |
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